July 18, 2000

Agriculture Takes Its Turn in the Genome Spotlight

By CAROL KAESUK YOON

	Xylella Fastidiosa Genome Project
	An electron micrograph of the bacterium Xylella fastidiosa.
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n a scientific first, and a coup for science in Brazil, a team of more than 200 researchers there has for the first time deciphered the complete DNA sequence of an organism that causes a plant disease.

Though other genome sequencing efforts -- for example, in humans or the laboratory staple fruit fly -- have attracted more attention, the Brazilian target, an odd little bacterium known as Xylella fastidiosa, distinguishes itself as the first to be decoded of the countless nasty species that together cost farmers and foresters many billions of dollars each year. This particular organism can cause diseases in oranges, grapes, almonds, plums, peaches, alfalfa, oaks, elms and other plants.

"Everyone is quite thrilled," said Dr. Andrew Simpson, a molecular biologist at the Ludwig Institute for Cancer Research in São Paulo, Brazil, and one of the team leaders. "It's probably the biggest ever scientific project in Brazil."

The team has been feted by the president of Brazil and serenaded by orchestras, and a new scientific prize was invented just to be given to the team. It was an achievement for developing nations' science as well, Dr. Simpson said, as this was the first complete sequence to come from outside the United States, the United Kingdom or Japan.

The consortium of scientists unveiled the full genome sequence of this bacterium in the current issue of the journal Nature.

Scientists said xylella's genome has already begun teaching biologists lessons about how pathogens evolve and about the destruction they cause. By revealing exactly which proteins this bacterium enlists to build itself and live its life, the complete sequence has also begun pointing the way toward methods for curbing this particular strain of the bacterium that attacks orange trees.

The report contains surprises, including the presence of genes thought to be peculiar to animal pathogens and a complete lack of some genes thought to be essential to plant disease organisms.

"It's going to be the standard against which all subsequent studies will be compared," said Dr. Edwin Civerolo, a plant pathologist with the U.S.D.A. Agricultural Research Service at the University of California at Davis. "It gives you the basis for designing novel and unique strategies for dealing with the disease, things we'd never thought of before."

Perhaps most surprising is that all this insight has come from an organism about which almost nothing was previously known.

Dr. Alan Collmer, a plant pathologist at Cornell University, called the new study "a big deal," adding: "This is a complete parts inventory for the bacterium. It's a remarkable demonstration of the power of genomics to give you an instant insight into an organism like this that was previously a black box. It's a revolutionary first step to take."

Scientists have typically sequenced the genomes of organisms that had already been intensively studied. But researchers said the new work illustrates the power of genome sequencing as the first step, rather than the last, in the path of knowledge, particularly for organisms whose biology is largely a mystery.

While designated a single species, Xylella fastidiosa is made up of numerous strains, each of which specializes in victimizing a different kind of plant. Researchers in Brazil, financed in part by the $4 billion a year orange juice industry, studied a strain that attacks orange trees after being injected into the plant by insects known as sharpshooter leafhoppers.

Once injected, xylella lives hidden in the plant's circulatory system, a network of water-conducting tissues known as the xylem. Hard to observe or collect and happiest inside a leafhopper or a plant, the bacterium is fastidious and hard to grow in the laboratory -- hence its name, fastidiosa. So though the diseases caused by xylella can be severe -- in California, vineyards lose tens of millions of dollars each year to the bacterium -- little was known about the biology of this bug.

Much has been learned now that the sequences of xylella's 2,800 genes are in hand.

Dr. Simpson said one of the biggest surprises was finding genes like those in animal pathogens, in particular three that were very similar to those in the bacterium that causes meningitis in humans, genes that help bacteria to gain a foothold in their host.

"Nobody suspected they'd be in these bacteria," said Dr. Simpson, who said the finding suggests that there may be common themes in disease-causing bacteria, irrespective of who the bacteria are attacking.

Other curious interlopers are the 83 genes from viruses that came in, infected the bacterium and left their DNA behind. These viruses also left DNA they had stolen from bacteria that cause diseases in animals, including humans. Dr. Simpson suggested that such wholesale importation of genes from other pathogens might be what turned xylella from benign to disease-causing.

The researchers also discovered that xylella has a penchant for sequestering iron, something that may explain the anemic, yellowing leaves symptomatic of the disease. One possibility for curbing the disease, said Dr. Simpson, was changing irrigation regimes to decrease the amount of iron available in these plants.

Any hint of a cure will be welcomed as farmers have few weapons against this class of diseases.

"Take, for example, citrus canker," another bacterial disease of orange trees, Dr. Collmer said. "It's the year 2000 and they handle that by burning the orchard. That is a brutal indicator of just how much at the mercy we are of these bacteria."

The most surprising discovery, however, has been what is not there. All other disease-causing bacteria share a complex of genes that allows them to inject specialized proteins that determine what kind of host species a bacterium can successfully attack. But while this system has been considered fundamental to causing disease, xylella wreaks havoc just fine without it.

In fact xylella's sequence is small, a mere one-thousandth the size of the human genome, and 24 bacteria (not causing plant disease) had already beat it to the finish line with little fanfare in their respective countries. But researchers said xylella's completion was worth a bit of hoopla as it marks not only the revelation of a new genome, but the entry of a surprising new player in a field dominated by developed nations.

"This enabled them to launch a genomics industry in Brazil," Dr. Collmer said. "I think they should celebrate."