Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling

J Exp Bot. 2016 Jul;67(14):4231-40. doi: 10.1093/jxb/erw217. Epub 2016 Jun 4.


Two maize phytochrome-interacting factor (PIF) basic helix-loop-helix (bHLH) family members, ZmPIF3.1 and ZmPIF3.2, were identified, cloned and expressed in vitro to investigate light-signaling interactions. A phylogenetic analysis of sequences of the maize bHLH transcription factor gene family revealed the extent of the PIF family, and a total of seven predicted PIF-encoding genes were identified from genes encoding bHLH family VIIa/b proteins in the maize genome. To investigate the role of maize PIFs in phytochrome signaling, full-length cDNAs for phytochromes PhyA2, PhyB1, PhyB2 and PhyC1 from maize were cloned and expressed in vitro as chromophorylated holophytochromes. We showed that ZmPIF3.1 and ZmPIF3.2 interact specifically with the Pfr form of maize holophytochrome B1 (ZmphyB1), showing no detectable affinity for the Pr form. Maize holophytochrome B2 (ZmphyB2) showed no detectable binding affinity for PIFs in either Pr or Pfr forms, but phyB Pfr from Arabidopsis interacted with ZmPIF3.1 similarly to ZmphyB1 Pfr. We conclude that subfunctionalization at the protein-protein interaction level has altered the role of phyB2 relative to that of phyB1 in maize. Since the phyB2 mutant shows photomorphogenic defects, we conclude that maize phyB2 is an active photoreceptor, without the binding of PIF3 seen in other phyB family proteins.

Keywords: Arabidopsis; PIF; bHLH; maize; phyB; phytochrome; subfunctionalization..

Publication types

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

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis / physiology
  • Basic Helix-Loop-Helix Transcription Factors / genetics
  • Basic Helix-Loop-Helix Transcription Factors / physiology*
  • Biological Evolution
  • Cloning, Molecular
  • DNA, Plant / genetics
  • Immunoprecipitation
  • Phylogeny
  • Phytochrome / physiology*
  • Plant Proteins / genetics
  • Plant Proteins / physiology
  • Sequence Alignment
  • Signal Transduction / physiology
  • Two-Hybrid System Techniques
  • Zea mays / genetics
  • Zea mays / metabolism*
  • Zea mays / physiology


  • Basic Helix-Loop-Helix Transcription Factors
  • DNA, Plant
  • Plant Proteins
  • Phytochrome