After isolating the normal version of this gene, Tao pinpointed its protein product and began exploring its function. Realizing the protein was an enzyme that catalyzes changes to small molecules such as amino acids, Tao and Chory turned to Salk colleague, HHMI investigator Joseph P. Noel, an expert in determining the function of plant enzymes. Noel and Chory reasoned that the enzyme might be involved in the biosynthesis of auxin, a hormone other studies have hinted plays a role in shade avoidance.

Their instincts were right. A series of experiments revealed that the sav3 plants made less auxin, and that adding auxin allowed them to shoot up in the shade. They named the enzyme after its function—TAA1, for tryptophan aminotransferase of Arabidopsis. The results appeared in the April 4, 2008, issue of Cell.

“In the shade, wild-type plants make more auxin,” Chory explains. “It seems that sav3 plants can't do that.” TAA1, they found, is integral to the synthesis of auxin that's triggered by plant shade.

		While a plant's response to shade is quick—it only takes an hour for changes to begin—a plant takes its time to respond to other environmental cues, and with good reason, says HHMI investigator Joanne Chory. “If a cloud comes over and you're a plant, do you want to start behaving like it's night? No. If there's a lightning flash in the middle of the night do you want to start behaving like it's day? No.” In a paper published in February in PLoS Genetics, Chory and colleagues revealed new information about how plants turn on different sets of genes at different times of the day and night, by slowly taking into account their environment. They found that a full 89 percent of Arabidopsis genes cycle in response to temperature, light, and circadian variations throughout a 24-hour cycle.

Studying the genes and proteins that cause shade avoidance could help plant biologists eventually create plants that don't avoid shade, she says. These plants would still need light but wouldn't overreact to just a little shade. Instead, they would be green, lush, and healthy even in crowded conditions.

“In modern agriculture, farmers sow crops very densely,” she explains. “The plants are always shading each other.” While healthy competition is a good thing when it comes to the natural selection of plants over time, a constant state of shade avoidance is not good because shaded plants produce fewer seeds, says Chory. “If the seed is what you're eating—like rice—there will be loss of yield.”

Yield is becoming increasingly important, says Chory, noting that by 2050 the world population is projected to exceed 9 billion. “It's all about sustainability,” she says. “You have to feed all these people, plus today food crops have to compete with energy crops.”

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