April 2010

Most animals, including ourselves, use sophisticated eyes to see light. The light-sensing mechanism in these eyes uses a specialized molecule that absorbs light and changes shape. You might be surprised to hear that plants also see light, and they use a similar chemical trick to see it. They build phytochrome proteins that enfold a light-sensing chromophore, which also changes shape when it absorbs a photon of light. These phytochromes, along with several other types of light-sensing proteins, are essential for the life of the plant. They allow plants to sense the levels and location of light, and thus maximize their ability to absorb the light for photosynthesis.

Light and Shade

Phytochromes are particularly adept at sensing the difference between full sunlight and shade. Phytochromes adopt two different states, termed Pr and Pfr. The Pr state is best at absorbing red light, which is found in full-sun conditions. When it absorbs red light, phytochrome converts to the Pfr state, which is better at absorbing far-red light. Far-red light is more indicative of shade, which is typically depleted of red light. The Pfr state can then convert back to the Pr state either by absorbing far-red light, or if it is in the dark for a while, by slow thermal conversion. Thus, this switch between Pr and Pfr states allows the plant to see if it is in the sun or the shade.

Taking Action

Of course, the plant needs to make use of this information once it gets it. Switching of phytochrome to the Pfr state launches a host of changes in the plant, causing it, for instance, to bend or grow towards the light. Phytochrome is normally found in the cytoplasm of the plant cell, but when it converts to the Pfr state, it moves to the nucleus and modulates the expression of many genes responsible for growth and shape of the plant.

Light-sensing Machinery

Researchers at the CESG have revealed the atomic basis of the light-sensing machinery in phytochromes. They have recently solved the structure of an unusually small phytochrome in both the Pr and Pfr states. The small size of the phytochrome was important in this study: it allowed the researchers to solve the structure quickly using NMR spectroscopy. The structure of the Pr state was solved first (PDB entries 2k2n and 2koi), then the protein was irradiated with red light during the NMR experiment. This produced a mixture of half Pr and half Pfr, which was used to solve the structure of the Pfr state (PDB entry 2kli, shown here). The structures show that the motion of the chromophore is completely different than what was expected.

Phytochrome (PDB entries 2koi and 2kli)

The chromophore of phytochrome (in green) is derived from a heme group, which has been chemically modified to form a string of four connected rings. The ring at one end is covalently attached to a cysteine amino acid in the protein (shown in yellow), gluing the chromophore in place inside the protein. When the chromophore absorbs light, one bond (colored here in red) flips its conformation and causes a 90 degree rotation of the ring attached to the cysteine (this ring is colored brighter green here). The motion of this ring came as a surprise, since previous work had lead researchers to think that the ring at the opposite end of the chromophore was the one that flipped. Use the buttons below to switch between the two structures.

display: Pr State   Pfr State  


  1. Ulijasz, A. T., Cornilescu, G., Cornilescu, C. C., Zhang, J., Rivera, M., Markley, J. L. and Vierstra, R. D. (2008) Structural basis for the photoconversion of a phytochrome to the activated Pfr form. Nature 463, 250-254.
  2. Cornilescu, G., Ulijasz, A. T., Cornilescu, C. C., Markley, J. L. and Vierstra, R. D. (2008) Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. J. Mol. Biol. 383, 403-413.
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  4. Wagner, J. R., Brunselle, J. S., Forest, K. T. and Vierstra, R. D. (2005) A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438, 325-331.
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