Allosteric deactivation of PIFs and EIN3 by microproteins in light control of plant development

Abstract

Buried seedlings undergo dramatic developmental transitions when they emerge from soil into sunlight. As central transcription factors suppressing light responses, PHYTOCHROME-INTERACTING FACTORs (PIFs) and ETHYLENE-INSENSITIVE 3 (EIN3) actively function in darkness and must be promptly repressed upon light to initiate deetiolation. Microproteins are evolutionarily conserved small single-domain proteins that act as posttranslational regulators in eukaryotes. Although hundreds to thousands of microproteins are predicted to exist in plants, their target molecules, biological roles, and mechanisms of action remain largely unknown. Here, we show that two microproteins, miP1a and miP1b (miP1a/b), are robustly stimulated in the dark-to-light transition. miP1a/b are primarily expressed in cotyledons and hypocotyl, exhibiting tissue-specific patterns similar to those of PIFs and EIN3. We demonstrate that PIFs and EIN3 assemble functional oligomers by self-interaction, while miP1a/b directly interact with and disrupt the oligomerization of PIFs and EIN3 by forming nonfunctional protein complexes. As a result, the DNA binding capacity and transcriptional activity of PIFs and EIN3 are predominantly suppressed. These biochemical findings are further supported by genetic evidence. miP1a/b positively regulate photomorphogenic development, and constitutively expressing miP1a/b rescues the delayed apical hook unfolding and cotyledon development of plants overexpressing PIFs and EIN3. Our study reveals that microproteins provide a temporal and negative control of the master transcription factors' oligomerization to achieve timely developmental transitions upon environmental changes.

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

“…phyB interacts with both EIN3 and EBF proteins, which facilitates EBF‐targeted EIN3 degradation in a light‐dependent manner (Shi et al, 2016b). Recently, Wu et al (2020) found that PIF transcription factors and EIN3 can form functional oligomers by self‐interaction. Two microproteins, miP1a and miP1b, interact with and disrupt the self‐association and oligomerization of PIFs and EIN3, suppressing the DNA‐binding ability and the transcriptional activity of PIFs and EIN3 (Wu et al, 2020).…”

“…Recently, Wu et al (2020) found that PIF transcription factors and EIN3 can form functional oligomers by self‐interaction. Two microproteins, miP1a and miP1b, interact with and disrupt the self‐association and oligomerization of PIFs and EIN3, suppressing the DNA‐binding ability and the transcriptional activity of PIFs and EIN3 (Wu et al, 2020). Interestingly, protein degradation regulation has been found to occur in nearly every step of the canonical ethylene signaling pathway.…”

PIF4 and PIF4-Interacting Proteins: At the Nexus of Plant Light, Temperature and Hormone Signal Integrations

“…Increasing studies have revealed that individual BBX protein has different functions. BBX4 and BBX21-BBX23 are positive regulators for light signaling, whereas BBX19, BBX24, BBX25 and BBX28-BBX32 inhibit photomorphogenesis [ 20 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 ]. Some BBXs form a transcriptional regulatory network with ELOGATED HYPOCOTYL 5 (HY5) through affecting HY5 activity to regulate photomorphogenic development.…”

Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature

“…Another interesting example of a BBX protein involved in regulation of hypocotyl growth is BBX31/microprotein 1a (miP1a), which can either promote or repress photomorphogenesis depending on the light context: BBX31 inhibits photomorphogenesis induced by R, FR, or B in hypocotyls, while it promotes UV‐B‐mediated growth repression (Heng et al ., 2019; Yadav et al ., 2019). It is possible that BBX31 inhibits hypocotyl growth in response to UV‐B by binding to PIFs and inhibiting their oligomerization (Wu et al ., 2020). Specifically, it has been demonstrated that BBX31, as well as its close homolog BBX30/miP1b, can interact with PIF3 and reduce its assembly into tetramers, thus inhibiting the ability of this PIF to activate the expression of genes such as PIL1 (Wu et al ., 2020).…”

“…It is possible that BBX31 inhibits hypocotyl growth in response to UV‐B by binding to PIFs and inhibiting their oligomerization (Wu et al ., 2020). Specifically, it has been demonstrated that BBX31, as well as its close homolog BBX30/miP1b, can interact with PIF3 and reduce its assembly into tetramers, thus inhibiting the ability of this PIF to activate the expression of genes such as PIL1 (Wu et al ., 2020). Notably, another BBX protein, BBX4, also binds PIF3 and inhibits its ability to activate target gene expression, which explains its negative effect on hypocotyl growth in R (Datta et al ., 2006; Heng et al ., 2020).…”