Into the light: Structure of Phytochrome

Light is one of the most important environmental stimuli for plants, controlling developmental processes such as germination, flowering as well as gene expression, circadian rhythms and metabolism [See IA PoO lectures]. Plants sense red light using the receptor phytochrome (PHY), which contains the chromophore phytochromobilin (PΦB). Crystal structures for bacterial phytochromes have been published, but until recently the 3D structure of the plant receptor protein was unknown. However, a group from the University of Wisconsin-Madison published the crystal structure of PHYB from the model plant Arabidopsis thaliana in PNAS last year, allowing much greater insight into how this fundamental receptor works.

Crystal structure of PHYB from Arabidopsis thaliana.
Crystal structure of PHYB from Arabidopsis thaliana.

Phytochrome signalling relies on the fact that PHY alternates between the less active form Pr, and the active form Pfr, a transition which is stimulated by the absorption of red light. Pfr then migrates from the cytosol to the nucleus where it interacts with proteins that regulate gene expression, such as the PHYTOCHROME INTERACTING FACTORS (PIFS). The researchers crystallised PHYB in the Pr form and solved its structure, revealing it to be a globular protein with a number of different domains, which assembles as a homodimer (see image).

The phytochromobilin (PΦB) is covalently linked to the protein a cystiene residue (C357) in the GAF domain via a thioester bond. It is known from previous studies that when the Pr to Pfr transition occurs, PΦB rotates. The authors propose a model where this rotation PΦB forces a conformational change in the protein by disrupting an interaction between an aspartate (D307) in the GAF domain and an arginine (R582) in the PHY domain. In the Pr form these interact, which stabilises a hairpin structure (highlighted in orange on the left hand side of the crystal structure). When PΦB is in the Pfr form this hairpin is disrupted, so a helical structure forms instead. This change in the surface structure of the protein will then presumably cause it to interact differently with other proteins including the PIFs.

Model for Phytochrome sigalling. In the Pr form (left) a β-hairpin forms between in the protein, but in the Pfr form this hairpin is disrupted by the rotation of the chromophore, so a helical structure forms instead. Image reproduced from PNAS, and then annotated.
Model for Phytochrome sigalling. In the Pr form (left) a β-hairpin forms between in the protein, but in the Pfr form this hairpin is disrupted by the rotation of the chromophore, so a helical structure forms instead. Image reproduced from PNAS, and then annotated.

Without having the structure of the Pfr form of the protein this model cannot be confirmed at present, but the research does give the best insights thus far into how light perception works in plants.

Reference: Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Burgie et al. (2014) P.N.A.S. 111(28):10179-84 DOI: 10.1073/pnas.1403096111

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