A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors

Plant Cell. 2004 Nov;16(11):3033-44. doi: 10.1105/tpc.104.025643. Epub 2004 Oct 14.


The phytochrome (phy) family of sensory photoreceptors (phyA to phyE) in Arabidopsis thaliana control plant developmental transitions in response to informational light signals throughout the life cycle. The photoactivated conformer of the photoreceptor Pfr has been shown to translocate into the nucleus where it induces changes in gene expression by an unknown mechanism. Here, we have identified two basic helix-loop-helix (bHLH) transcription factors, designated PHYTOCHROME-INTERACTING FACTOR5 (PIF5) and PIF6, which interact specifically with the Pfr form of phyB. These two factors cluster tightly with PIF3 and two other phy-interacting bHLH proteins in a phylogenetic subfamily within the large Arabidopsis bHLH (AtbHLH) family. We have identified a novel sequence motif (designated the active phytochrome binding [APB] motif) that is conserved in these phy-interacting AtbHLHs but not in other noninteractors. Using the isolated domain and site-directed mutagenesis, we have shown that this motif is both necessary and sufficient for binding to phyB. Transgenic expression of the native APB-containing AtbHLH protein, PIF4, in a pif4 null mutant, rescued the photoresponse defect in this mutant, whereas mutated PIF4 constructs with site-directed substitutions in conserved APB residues did not. These data indicate that the APB motif is necessary for PIF4 function in light-regulated seedling development and suggest that conformer-specific binding of phyB to PIF4 via the APB motif is necessary for this function in vivo. Binding assays with the isolated APB domain detected interaction with phyB, but none of the other four Arabidopsis phys. Collectively, the data suggest that the APB domain provides a phyB-specific recognition module within the AtbHLH family, thereby conferring photoreceptor target specificity on a subset of these transcription factors and, thus, the potential for selective signal channeling to segments of the transcriptional network.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs / genetics
  • Amino Acid Motifs / physiology
  • Arabidopsis / genetics
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / isolation & purification
  • Arabidopsis Proteins / metabolism*
  • Basic Helix-Loop-Helix Transcription Factors
  • Binding Sites / genetics
  • DNA, Complementary / genetics
  • DNA, Complementary / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / isolation & purification
  • DNA-Binding Proteins / metabolism
  • Helix-Loop-Helix Motifs / physiology*
  • Light
  • Molecular Sequence Data
  • Mutation / genetics
  • Photic Stimulation
  • Photoreceptor Cells / metabolism*
  • Phytochrome / metabolism*
  • Phytochrome B
  • Protein Binding / genetics
  • Sequence Homology, Amino Acid
  • Sequence Homology, Nucleic Acid
  • Signal Transduction / genetics
  • Transcription Factors / genetics
  • Transcription Factors / isolation & purification
  • Transcription Factors / metabolism*


  • Arabidopsis Proteins
  • Basic Helix-Loop-Helix Transcription Factors
  • DNA, Complementary
  • DNA-Binding Proteins
  • PHYB protein, Arabidopsis
  • PIF4 protein, Arabidopsis
  • PIF5 protein, Arabidopsis
  • PIF6 protein, Arabidopsis
  • Transcription Factors
  • Phytochrome
  • Phytochrome B