Phytochromes

Phytochromes are a class of light-sensing proteins that detect red and far-red light in plants and some microorganisms. They are bilin-containing photoreceptors that regulate key developmental processes including seed germination, seedling de-etiolation, shade-avoidance responses, flowering time, and circadian rhythms. Phytochromes exist as gene families in many species, with distinct members providing complementary light sensing and signaling functions.

Structure and chromophore: Each phytochrome contains an N-terminal photosensory core module comprising PAS, GAF, and PHY domains that bind a linear tetrapyrrole chromophore. In plants, the chromophore is phytochromobilin; in many bacteria and fungi, it is biliverdin. The chromophore is covalently linked to a conserved cysteine residue and undergoes light-driven isomerization between the red-absorbing form Pr and the far-red-absorbing form Pfr. Red light converts Pr to the biologically active Pfr form, while far-red light and thermal reversion return the protein to Pr.

Signal transduction: Photoisomerization triggers large conformational rearrangements that alter the phytochrome's interactions with signaling partners. In plants, these changes affect transcription factors such as PIFs and other regulators, leading to changes in gene expression and development. In bacteria, bacteriophytochromes typically act through two-component signaling systems, modulating kinase activity in response to light.

Diversity and significance: In flowering plants, several phytochromes (for example, phyA, phyB, phyC, phyD, phyE in Arabidopsis) contribute to light responses with different spectral sensitivities and action spectra. Phytochromes are widespread beyond plants, including bacteria and fungi, where they provide a red/far-red light switch for ecological adaptation. Research on phytochromes informs basic science and has potential applications in agriculture and synthetic biology.