Phytochrome is known as a photoreversible photoreceptor, meaning that it can change forms from the inactive to active states (and vice-versa) by absorbing distinct wavelengths of light. When it absorbs red light, the phytochrome complex changes shape and becomes activated. At the same time, this change in shape means that it no longer absorbs in the red part of the spectrum, but its absorbance maximum has shifted to the far-red part of the spectrum. Interception of a photon in the far-red energy range will cause the complex to change shape back to the red-absorbing form, as will a prolonged period in the dark.

When embryo-dormant seeds with thin seed coats are exposed to red light in the environment, they are induced to begin germinating through the activation of phytochrome. And because phytochrome is photo-reversible, germination can be halted if the embryo detects that it is in the presence of lower energy far-red light. This watershed observation about germination was one of the first indications of the existence of the phytochrome pathway during the 1950’s and 1960’s:

Seed hit with red light germinated unless it was then hit with far-red; but if red again ensued, it would germinate. Incredibly, all that mattered was which color came last even if the seed was struck by 100 alternating cycles of red and far-red.

Phytochrome structure

Functional phytochrome molecules are composed of a protein component with a pigment molecule bound tightly to it. The apoprotein, as it is known, is encoded by one of five genes in Arabidopsis, and the chromophore, as the pigment is known, is a bilin-type pigment similar in structure to a chlorophyll precursor. Furthermore, phytochromes pair up with another phytochrome to form a dimer. This interaction happens between amino acids at the amino-terminal end of the protein. The other end of the protein, the carboxy-terminal end, shows homology to bacterial histidine kinase domains, but it isn’t clear whether phytochromes act as kinases themselves when activated.

Phytochrome signaling

Upon perception of red light, phytochrome molecules undergo a conformational change and appear to traffic to the nucleus, where they can interact with partner proteins. One such partner is PIF3 (Phytochrome Interacting Factor 3), a basic helix-loop-helix transcription factor that binds to the promoter of light-regulated genes. At least several of the genes regulated by PIF3 encode transcription factors themselves. In addition, phytochrome has been shown to increase expression of at least one gene encoding an enzyme in the GA biosynthetic pathway. GA biosynthesis, in turn, can promote the expression of hydrolytic enzymes associated with energy mobilization and uptake by the embryo.


Toyomasu et al. (1998) Phytochrome Regulates Gibberellin Biosynthesis during Germination of Photoblastic Lettuce Seeds. Plant Physiol 118: 1517-1523