Plant biologists determine molecular ‘blueprint’, showing how plants observe light

For survival, plants depend on their ability to detect light. Plants, unlike animals, do not have photoreceptors in their eyes to receive and transmit messages from visual inputs. Plants are instead covered with a system of light-sensing photoreceptors that detect various wavelengths of light, enabling them to control their lifecycles and adapt to changing environmental conditions.

Researchers from the Van Andel Institute and Washington University have finally discovered the molecular structure of one of these critical photoreceptors, PhyB, indicating an entirely different structure than previously thought. The discoveries, which were published in the journal Nature, could have ramifications for agricultural and “green” biotech methods.

Photoreceptors, such as PhyB, help plants sense and respond to the world around them by influencing life-sustaining processes such as shade avoidance, seed germination, determination of flowering time, and development of chloroplasts, which convert light into usable energy.”

Huilin Li, PhD, Study Co Corresponding Author and Professor, Van Andel Institute

“Our new structure sheds light onto how PhyB works and has potential for a host of applications in agriculture, renewable energy and even in cellular imaging,” Li added.

Understanding PhyB’s shape is crucial since it has a direct effect on how it connects with other molecules to transmit light changes and help plants adapt by causing changes in gene expression. Previous studies on PhyB only provided a truncated image of the complete molecule, rather than a comprehensive depiction.

Li and study co-corresponding author Richard D. Vierstra, Ph.D., of Washington University, used one of the most researched plants on the planet, Arabidopsis thaliana, to create a near-atomic resolution image of PhyB. Because it reproduces rapidly, is tiny, and easy to manage, this small blooming plant is a good model for research.

The study team captured roughly 1 million particle images of PhyB coupled to its natural chromophore—a molecule that emits a specific color of light—using VAI’s high-powered cryo-electron microscope, or cryo-EM. They then reduced the photos to 155,000, which they utilized to create a comprehensive representation of PhyB’s structure at a 3.3 Ångstrom near-atomic level.

Instead of the parallel structure discussed in the earlier investigations, researchers discovered a sophisticated 3D structure with both parallel and anti-parallel portions. The findings imply that PhyB can magnify modest changes in light-sensing chromophore molecules and modify its shape dramatically in response, signaling to the plant that light is available.

The discovery is the culmination of a decade of work between Li and Vierstra, and it completely changes our understanding of PhyB and phytochromes, the receptor family to which PhyB falls. PhyB and other phytochromes were formerly thought to be identical to those found in single-celled organisms such as bacteria.

The new findings challenge that idea and establish the groundwork for more research into the essentials of PhyB and phytochrome function.

The study’s co-first authors are VAI’s Hua Li, PhD, and Washington University’s Sethe Burgie, PhD Washington University’s Zachary T.K. Gannam, PhD, is also a contributor. The David Van Andel Advanced Cryo-Electron Microscopy Suite and VAI’s Cryo-EM Core collaborated to acquire cryo-EM data.