Bottom-up Assembly of the Phytochrome Network

Abstract

Plants have developed sophisticated systems to monitor and rapidly acclimate to environmental fluctuations. Light is an essential source of environmental information throughout the plant’s life cycle. The model plant Arabidopsis thaliana possesses five phytochromes (phyA-phyE) with important roles in germination, seedling establishment, shade avoidance, and flowering. However, our understanding of the phytochrome signaling network is incomplete, and little is known about the individual roles of phytochromes and how they function cooperatively to mediate light responses. Here, we used a bottom-up approach to study the phytochrome network. We added each of the five phytochromes to a phytochrome-less background to study their individual roles and then added the phytochromes by pairs to study their interactions. By analyzing the 16 resulting genotypes, we revealed unique roles for each phytochrome and identified novel phytochrome interactions that regulate germination and the onset of flowering. Furthermore, we found that ambient temperature has both phytochrome-dependent and -independent effects, suggesting that multiple pathways integrate temperature and light signaling. Surprisingly, none of the phytochromes alone conferred a photoperiodic response. Although phyE and phyB were the strongest repressors of flowering, both phyB and phyC were needed to confer a flowering response to photoperiod. Thus, a specific combination of phytochromes is required to detect changes in photoperiod, whereas single phytochromes are sufficient to respond to light quality, indicating how phytochromes signal different light cues.

Heat Stress Factors Expressed during Seed Maturation Differentially Regulate Seed Longevity and Seedling Greening

“…Thus, A9 would link seed maturation and seedling photomorphogenesis by acting on photoreceptors for light with wavelengths placed at both ends of the visible spectrum: CRY1 (for blue light; as confirmed by the results in Figures 4 and 5), in addition to PHYA (for far-red light) and PHYB (for red light) as reported earlier [17]. Tables S1 and S2 (where some important gene examples are outlined) indicate the potential upregulation of additional light receptors, including different phytochromes (PHYC for red light, [12][13][14]31]) and phototropins (PHOT2 for blue light, [16]). In connection with early photomorphogenesis and seedling establishment, responses to blue light mainly mediated by CRY1 (and also by PHOT) receptors are crucial for inducing massive gene expression changes that occur after extensive chromatin and nuclear architecture reorganization [32,33].…”

Combining Digital Imaging and Genome Wide Association Mapping to Dissect Uncharacterized Traits in Plant/Pathogen Interactions

“…More importantly, using 407 new lesion-related traits for GWAS identified new genes involved in resistance to B. cinerea 408 that had not previously been identified. This includes genes involved in light signal transduction, 409 LUX, PHOT1 and PHYE, as well as sulfur transport (Clack et al, 1994;Devlin et al, 1998;Briggs 410 and Christie, 2002;Halliday and Whitelam, 2003;Kataoka et al, 2004;Hazen et al, 2005;Zuber 411 et al, 2010a;Nusinow et al, 2011;Sanchez-Lamas et al, 2016). The three light-related genes 412 affected different lesion traits with PHOT1 being specific to lesion size, PHYE altering lesion size 413 and yellowing while LUX and the sulfur transporter specifically altered lesion size (Figure 7).…”

Differential phosphorylation of the N‐terminal extension regulates phytochrome B signaling

“…Red and far-red light is detected by the phytochrome (phy) family of sensory photoreceptors, which in Arabidopsis thaliana comprises five members (phyA-E) with different but also partially overlapping functions (S anchez-Lamas et al, 2016). Red and far-red light is detected by the phytochrome (phy) family of sensory photoreceptors, which in Arabidopsis thaliana comprises five members (phyA-E) with different but also partially overlapping functions (S anchez-Lamas et al, 2016).…”