Plants survive by getting access to light. And according to a new study led by Salk Institute scientists, plants can also sense subtle qualities in the spectrum of light that hits them, using that information to guide their growth.

A lack of blue light, detected by certain proteins, causes plants to activate growth-promoting genes, according to the study, published Dec. 24 in Cell. This mechanism acts along with a previously known one that reacts when light is deficient in the red portion of the spectrum, causing release of a growth hormone called auxin.

Moreover, the genes that respond under low blue conditions differ from those that respond to a lack of red to far-red light. This means plants have a second, independent system that prods them to grow when light of a certain color is lacking -- something not known before.

Researchers say this discovery might be used to modify the genes of plants to optimize their yield. Shaded tomato plants, for example, could be made to channel more energy into growing tomatoes and less into making leaves.


The senior author is Joanne Chory, a renowned plant researcher whose lab has made a number of fundamental discoveries about plants, including their use of a steroid hormone to reach their mature size. Chory plumbs the biology of the model plant Arabidopsis, used in this study.

Chory is also a Howard Hughes Medical Institute investigator and holder of the Howard H. and Maryam R. Newman Chair in Plant Biology. The chair, endowed in 2009, was the first to be funded under a campaign led by Salk Board Chairman Irwin Jacobs and his wife, Joan.

Ullas Pedmale, a Salk research associate in Chory’s lab, is first author of the paper. He said he joined Chory’s lab specifically to work on this problem.

Ullas Pedmale ( / Salk Institute)


The selective response to blue and red light is rooted in the nature of photosynthesis. Red and blue happen to be the portions of the spectrum most efficiently absorbed by plants. So their deficiency, compared to light of other wavelengths, provides an environmental clue that other vegetation may be blocking light.

The logical reaction: Grow away from the shadow of the competing foliage. In what is known as shade avoidance response, plants redirect their energy away from storage and toward elongating stems and leafstalks, allowing the shaded plant to reach the light.

Auxin is one part of that response. Another, according to the study, is a set of proteins called cryptochromes that sense blue light, triggering genetic activity that also leads to growth.

Why plants use multiple ways to regulate what appears to be the same growth process isn’t clear, the researchers stated in the paper. It might have to do with the wide variety of growth responses observed, as well as the many differing shapes plants can take, they conjectured.


Life without a brain

Researchers discovered the second shade avoidance mechanism by testing Arabidopsis in a room with limited blue light. They placed normal Arabidopsis plants in the room along with mutated ones that lacked either the cryptochromes or two proteins that controls gene expression, called PIF transcription factors.

Normal and mutant Arabidopsis were grown under varying blue-light restricted conditions. Researchers studied the patterns of growth and looked at the molecular level at how the crytochromes, PIFs, and chromosomes interacted.

It’s an ingenious mechanism, Pedmale said. Moreover, it demonstrates how plants can adapt to their environment without that seemingly indispensable tool of animals: A brain.


The brain, the CPU, the master controller, explains many fundamental attributes of animals, especially mammals. Yet plants don’t appear to have a control center, Pedmale said. How the cellular “decisions” made throughout the plant unit to a harmonious response is not well understood.

Although nearly immobile on the macroscale, plants nevertheless are furiously active at a molecular level. They not only photosynthesize to capture energy, they produce myriad molecules that help in reproduction, fighting disease and even chemically summoning help when under attack by predators.

Plants are even “smart” enough to reduce their chemical defenses when insects eat shaded portions, he said. It’s almost as if the plant has calculated that its shaded portions aren’t worth defending, and will instead focus on growth where there’s light.

“Plants don’t have a brain, but they beautifully integrate all this information ... and they make a decision” Pedmale said. “So we have to figure out how this decision is made, and where the decision is made.”


Plants also differ from animals in how they determine their shape, Pedmale said.

“No two plants look alike, unlike us,” Pedmale said. “Our entire body plan is made in the womb, before we are born. We have five fingers on each hand, five toes on each foot. But plants wait, and decide according to what the environment is. They decide how many leaves they are going to put out. If a plant is shading them on one side, they’re not going to put out as many leaves on that side.”

“The reason is plants cannot run like us. They’re stuck in one place, so they need to keep changing their body plans to make the best use of the environment. Pathogens, light conditions, rain, humidity, roots ... play a major role.”

Pedmale said that when he joined Chory’s lab, he decided to examine how plants perceive a blue light deficiency and produce the same shade avoidance response as a lack of red light.


Cryptochromes were already known as blue-light sensors, Pedmale said, but the pathway linking their activity to directing a growth response wasn’t known, and that became the paper’s focus.

Similarities under the surface

Plant research at the Salk goes on in the shade of more prominent research on neuroscience and cancer. The work of Chory and colleagues such as Joseph Ecker have identified deep homologies with animals that could be of importance to human therapy.

One recent study Chory led identified how plant cells mark defective chloroplasts for removal. Chloroplasts bear similarities to mitochondria, and defective mitochondria in neurons plays a role in neurodegenerative diseases.


Work by Ecker and colleagues in plant epigenetics became the foundation for a study that identified novel epigenomic differences in mammalian neurons. They team identified a kind of methylation first identified in Arabidopsis.

In an interview, Ecker said his team found this peculiar kind of methylation -- the most abundant in neurons -- because they knew to look for it.

And so by connecting apparently disparate facts, science advances.