Residues Clustered in the Light-Sensing Knot of Phytochrome B are Necessary for Conformer-Specific Binding to Signaling Partner PIF3

Abstract

The bHLH transcription factor, PHYTOCHROME INTERACTING FACTOR 3 (PIF3), interacts specifically with the photoactivated, Pfr, form of Arabidopsis phytochrome B (phyB). This interaction induces PIF3 phosphorylation and degradation in vivo and modulates phyB-mediated seedling deetiolation in response to red light. To identify missense mutations in the phyB N-terminal domain that disrupt this interaction, we developed a yeast reverse-hybrid screen. Fifteen individual mutations identified in this screen, or in previous genetic screens for Arabidopsis mutants showing reduced sensitivity to red light, were shown to also disrupt light-induced binding of phyB to PIF3 in in vitro co-immunoprecipitation assays. These phyB missense mutants fall into two general classes: Class I (eleven mutants) containing those defective in light signal perception, due to aberrant chromophore attachment or photoconversion, and Class II (four mutants) containing those normal in signal perception, but defective in the capacity to transduce this signal to PIF3. By generating a homology model for the three-dimensional structure of the Arabidopsis phyB chromophore-binding region, based on the crystal structure of Deinococcus radiodurans phytochrome, we predict that three of the four Class II mutated phyB residues are solvent exposed in a cleft between the presumptive PAS and GAF domains. This deduction suggests that these residues could be directly required for the physical interaction of phyB with PIF3. Because these three residues are also necessary for phyB-imposed inhibition of hypocotyl elongation in response to red light, they are functionally necessary for signal transfer from photoactivated phyB, not only to PIF3 and other related bHLH transcription factors tested here, but also to other downstream signaling components involved in regulating seedling deetiolation. Plants monitor their environment for informational light signals that are used to direct adaptive morphogenic responses. The phytochrome (phy) family of photoreceptors are central to this process. Upon photoperception, phy molecules rapidly translocate to the nucleus where they interact with basic helix-loop-helix transcription factors, termed PIFs (phy-Interacting Factors), and induce gene-expression changes that control morphogenic responses. The molecular determinants in the phy protein responsible for direct intermolecular signal transfer from the activated photoreceptor to transduction partners are undefined. Using random mutagenesis of Arabidopsis phyB, coupled with a reverse-hybrid protein-interaction screen, we identified missense mutations in the N-terminal domain that abrogate the binding of the photoreceptor molecule to PIF3. A subset of these mutated phyB molecules retain the capacity for light-signal perception but are defective in the capacity to transduce that signal to PIF3 and other related PIFs. The mutated residues in these molecules are predicted to cluster at the surface of the protein in a structure termed the “light-sensing knot.” These residues are necessary for phyB-regulated growth in the living plant, establishing that the protein region identified appears to function as a component of the molecular interface responsible for direct signal transfer to transduction partners in the cell.