Photoreceptor signaling: when COP1 meets VPs

Abstract

How structurally distinct photoreceptors regulate evolutionarily diverse transcription factors to modulate common photoresponses is an intriguing question in plant biology. In this issue of The EMBO Journal, Lau et al demonstrate that COP1, the substrate receptor of E3 ubiquitin ligase CUL4^{COP 1‐ SPA s}, interacts with the diverse VP motif‐containing transcription factors and photoreceptors via its highly plastic WD40 domain. Light‐activated photoreceptors increase their affinity to COP1 to outcompete the COP1‐interacting transcription factors, allowing their accumulation and inducing photomorphogenic development of plants.

Plants possess many evolutionarily distinct photoreceptors that often regulate common photomorphogenic responses of plants. For example, seeds of dicotyledon plants germinated in the dark develop fast elongating hypocotyls (embryonic stem) and un‐expanded cotyledons (embryonic leaves) that contain etioplasts (undeveloped plastids). In response to light, different photoreceptors mediate similar photoresponsive gene expression changes, leading to suppression of hypocotyl elongation, promotion of cotyledon expansion, and conversion of etioplasts to chloroplasts. Given that different wavelengths of light exert similar photomorphogenic changes in plants, such as inhibition of hypocotyl growth, there must be a mechanism to convert different wavelength signals of light to the same developmental responses of plants. The gradual revelation of this mechanism started 27 years ago when an Arabidopsis mutant called cop1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) was identified (Deng et al, 1992). The loss‐of‐function cop1 mutants exhibit constitutive photomorphogenic phenotypes, such as suppressed hypocotyl elongation in the absence of light, suggesting that COP1 is a negative regulator of photomorphogenesis. Studies in the following decades demonstrated that COP1 acts as the substrate receptor of the E3 ubiquitin ligase CUL4^COP1‐SPAs to facilitate ubiquitination and degradation of various transcription factors required for photomorphogenesis (Lau & Deng, 2012; Podolec & Ulm, 2018). Remarkably, three out of five classes of plant photoreceptors, phytochromes, cryptochromes, and UVR8, mediate photoresponses at least partially by inhibition of the COP1 activity (Lau & Deng, 2012; Podolec & Ulm, 2018). However, the exact structural mechanisms underlying this photoreceptor–COP1–substrate tripartite interaction and how the evolutionarily distinct photoreceptors converge on the single hub protein COP1 remained unclear. In this issue of The EMBO Journal, a study from the Roman Ulm and Michael Hothorn's groups at University of Geneva solved, at least partially, these structure‐function problems (Lau et al, 2019).

COP1 is an evolutionarily conserved protein that contains three domains, the Zinc finger domain, the coiled‐coil domain, and the WD40 domain composed of seven‐bladed β propellers (Deng et al, 1992; Uljon et al, 2016). COP1 interacts with diverse light‐signaling transcription factors, such as the bZIP transcription factors HY5 (ELONGATED HYPOCOTYL 5) and HYH (HY5 HOMOLOG), BBX transcription factors CO/BBX1 (CONSTANS), COL3/BBX4, and STO/BBX24 (SALT TOLERANCE), and the bHLH transcription factor HFR1 (LONG HYPOCOTYL IN FAR‐RED 1), to regulate their stability in response to light (Lau & Deng, 2012). On the other hand, the UV‐B light receptor UVR8 and the blue light receptors CRY1 and CRY2 interact with COP1 to suppress its activity (Podolec & Ulm, 2018). An earlier study showed that three COP1‐interacting proteins bear a common sequence motif, referred to as VP, which contains two amino acids, valine–proline, as the invariable core, and that the VP motif may be a common COP1‐binding site (Holm et al, 2001). Lau et al (2019) showed that six transcription factors (HY5, HYH, CO, COL3, STO, and HFR1) and three photoreceptors (CRY1, CRY2, and UVR8) all possess the VP motifs. They examined the crystal structures of the complexes of the WD40 domain of COP1 (326 residues) and individual VP motifs (< 10 residues) of those nine COP1‐interacting proteins, demonstrating that the core residues of the VP motifs form the center of the COP1‐binding site, whereas the chemically diverse residues at the −3 and −2 position of the VP motifs act as anchor residues by inserting deeply into the VP‐binding cleft of COP1. These findings strongly argue that COP1 acts as a master regulator of photomorphogenesis due to the high structural plasticity of its WD40 domain that can accommodate sequence‐divergent VP motifs of either the substrates of the CUL4^COP1‐SPAs E3 ubiquitin ligase or the photoreceptors that inhibit the activity of COP1.

To gain further mechanistic insights into how photoreceptors inhibit the activity of COP1, Lau and the colleagues analyzed the complex structures and kinetics of protein–protein interactions among three sets of proteins: COP1, its transcription factor substrates, and the photoreceptors UVR8 and CRY2. In addition to the VP motif, other sites or regions of CRY2 and UVR8 participate in cooperative interaction to increase their affinity to COP1 by 200‐ to 1,000‐fold. In response to UV‐B or blue light, UVR8 and CRY2 undergo changes in the quaternary structure to become active (Rizzini et al, 2011; Wang et al, 2016), thus markedly increasing their affinity to COP1 to outcompete the substrates of COP1. For example, illumination with UV‐B light increases the affinity of UVR8 to COP1 to outcompete HY5 from interacting with COP1, leading to accumulation of HY5 and promotion of photomorphogenesis of young seedlings, whereas blue light exposure increases the affinity of CRY2 to COP1 to prevent COP1 from binding to CO, resulting in accumulation of CO and promotion of floral initiation in adult plants (Fig 1). It is fascinating that more than a dozen different proteins have co‐evolved this competitive photoreceptor–COP1–substrate tripartite interaction to regulate common photoresponses in plants.

Figure 1. A model depicting how photoreceptors regulate COP1 to promote photomorphogenesis.

In darkness (left panel), the UV‐B receptor UVR8, blue light receptor cryptochromes (CRYs), and red/far‐red light receptor phytochromes (PHYs) are inactive, and the VP motifs in UVR8 and CRYs are inaccessible; the COP1/SPAs complex interacts with the VP motif of the substrate transcription factors (TFs, grey) to facilitate their degradation (arrows), resulting in no or low transcription of the photoresponsive genes (cross). In response to the respective wavelengths of light (right panel), UVR8 and CRYs undergo monomerization or oligomerization, respectively, and conformational changes leading to exposure of the VP motifs to become active; the VP motifs of the active UVR8 and CRYs interact with the WD40 domain of COP1 (yellow) to outcompete and suppress its interaction with the VP motifs of transcription factors, resulting in their stabilization, active transcription of the target genes (waved lines), and plant photomorphogenesis. Phytochromes (PHYs) interact with SPAs to inhibit COP1 by different mechanisms not depicted in the figure.

The EMBO Journal (2019) 38: e102962