Obligate Heterodimerization ofArabidopsisPhytochromes C and E and Interaction with the PIF3 Basic Helix-Loop-Helix Transcription Factor

Abstract

Phytochromes are dimeric chromoproteins that regulate plant responses to red (R) and far-red (FR) light. The Arabidopsis thaliana genome encodes five phytochrome apoproteins: type I phyA mediates responses to FR, and type II phyB-phyE mediate shade avoidance and classical R/FR-reversible responses. In this study, we describe the complete in vivo complement of homodimeric and heterodimeric type II phytochromes. Unexpectedly, phyC and phyE do not homodimerize and are present in seedlings only as heterodimers with phyB and phyD. Roles in light regulation of hypocotyl length, leaf area, and flowering time are demonstrated for heterodimeric phytochromes containing phyC or phyE. Heterodimers of phyC and chromophoreless phyB are inactive, indicating that phyC subunits require spectrally intact dimer partners to be active themselves. Consistent with the obligate heterodimerization of phyC and phyE, phyC is made unstable by removal of its phyB binding partner, and overexpression of phyE results in accumulation of phyE monomers. Following a pulse of red light, phyA, phyB, phyC, and phyD interact in vivo with the PHYTOCHROME INTERACTING FACTOR3 basic helix-loop-helix transcription factor, and this interaction is FR reversible. Therefore, most or all of the type I and type II phytochromes, including heterodimeric forms, appear to function through PIF-mediated pathways. These findings link an unanticipated diversity of plant R/FR photoreceptor structures to established phytochrome signaling mechanisms.

The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS

“…We failed repeatedly to confirm the T-DNA insertion in an additional previously reported gnl allele, SALK_021362 (Mara and Irish 2008). ga1 (SALK_109115), gid1abc, pif1, pif3, pif1 pif3, pif1 pif3 pif4 pif5 (pif1345), PIF3:MYC(63), rga-24 gai-t6, and spy-3 mutants were described previously (King et al 2001;Silverstone et al 2007;Willige et al 2007;Leivar et al 2008;Clack et al 2009). …”

“…7C; Frazer et al 2004). We then immunoprecipitated PIF3:MYC(6x) to test whether GNC and GNL promoter fragments can be recognized by PIF3, at least when expressed from a highlevel constitutive promoter (Clack et al 2009). Indeed, we found that one predicted element of the GNC promoter as well as three predicted elements of the GNL promoter precipitate with PIF3:MYC(6x) (Fig.…”

A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light

“…Type II phys (phyB-E) form homo-and heterodimers that complicate interpretation of phenotypes of loss-offunction phy mutants and of gain-of-function YHB transgenics (Sharrock and Clack, 2004;Clack et al, 2009;Hu et al, 2009). The additive circadian defect of phyABD mutants compared with phyAB has been assumed to indicate an ability of phyD to provide light input into the circadian system in the absence of phyB (Devlin and Kay, 2000).…”

“…The ability of phyB-E to form homo-and heterodimers introduces complexity into the interpretation of individual phy mutant phenotypes (Sharrock and Clack, 2004;Clack et al, 2009;Hu et al, 2013). In addition, period length in phyABCDE mutants is modestly sensitive to different fluence rates of red light (Hu et al, 2013), suggesting that metabolic processes may complicate the assessment of the role of Phys in light input to the circadian clock.…”

“…Although recent studies on temperate grasses have established a direct role for phyC in photoperiod sensing (Chen et al, 2014;Woods et al, 2014), phyC has not been formally described as part of the circadian system in Arabidopsis. However, phyC is presumed to act similarly to phyE as a modulator of phyB activity since neither phyC nor phyE is capable of forming the homodimers necessary for signaling activity in Arabidopsis (Clack et al, 2009) or in rice (Oryza sativa; Xie et al, 2014), and instead, both function as heterodimers with other phys.…”