Dancing in the dark: darkness as a signal in plants

Abstract

Daily cycles of light and dark provide an organizing principle and temporal constraints under which life on Earth evolved. While light is often the focus of plant studies, it is only half the story. Plants continuously adjust to their surroundings, taking both dawn and dusk as cues to organize their growth, development and metabolism to appropriate times of day. In this review, we examine the effects of darkness on plant physiology and growth. We describe the similarities and differences between seedlings grown in the dark versus those grown in light-dark cycles, and the evolution of etiolated growth. We discuss the integration of the circadian clock into other processes, looking carefully at the points of contact between clock genes and growth-promoting gene-regulatory networks in temporal gating of growth. We also examine daily starch accumulation and degradation, and the possible contribution of dark-specific metabolic controls in regulating energy and growth. Examining these studies together reveals a complex and continuous balancing act, with many signals, dark included, contributing information and guiding the plant through its life cycle. The extraordinary interconnection between light and dark is manifest during cycles of day and night and during seedling emergence above versus below the soil surface.

Keywords: Arabidopsis; PIF; circadian; dark; growth; light; photobody; phytochrome; sugar.

Figure 1

. The Arabidopsis Circadian Clock. The circadian clock is diagrammed clockwise according to approximate time of maximal transcript level. The ring around the gene network diagram indicates the approximate light–dark cycle. late elongated hypocotyl (LHY) and circadian clock associated 1 (CCA1) transcripts peak in the morning, reveille (RVE) and pseudo-response regulator (PRR) transcripts rise sequentially from the late morning through afternoon, timing of cab expression 1 (TOC1) peaks in the early night, and gigantea (GI) and the members of the evening complex rise in the early-mid night. Internal cross-regulation of clock gene transcripts is indicated by arrowheads (positive regulation) or bars (negative regulation). For detailed description of clock function and input mechanisms, we direct the reader to Hsu & Harmer (2014); Jones (2009); McClung (2011) and Sanchez & Kay (2016).ELF, early flowering.

Figure 2.

Temporal gating of phytochrome-interacting factor (PIF) function by phytochromes, photobodies, and the circadian clock. During the day, active PHY-Pfr (green) suppress PIF levels and activity. In the dark, PHY-Pfr reverts to the inactive Pr form (grey). The rate of dark reversion likely depends on membership in photobodies (pink circles), with free PHY reverting more quickly than photobody associated PHY. In the late day and early night, PIF (blue) activity is repressed by timing of cab expression 1 (TOC1) and by photobody-associated PHY-Pfr. Later in the night, TOC1 is degraded, free PHY has reverted to Pr or is degraded, and the photobodies dissociate, thus relieving the repression of PIF abundance and activity. This coordinated derepression of PIF activity promotes hypocotyl growth at the end of the night.

Figure 3.

Oscillations of metabolites in light–dark cycles suggest dark-activated starch breakdown. (a) Model profiles of starch (solid black), maltose (solid blue), sucrose (solid green) and hydrogen peroxide ( H₂O₂ – dashed black) across a 12 h light, 12 h dark cycle. Photosynthesis keeps sucrose levels high during the day and simultaneously builds up starch granules. Reactive oxygen species, including H₂O₂, are high through the day, and begin to drop in the late day. At lights-off, starch degradation is rapidly initiated and there is a rapid increase in maltose. Sucrose levels drop quickly at lights-off but rebound as the starch reserves are freed, providing energy during the night. (b) A prospective model of a carbohydrate homeostasis control system. H₂O₂ inhibits the activity of key enzymes in both starch synthesis (AGPase) and degradation (SEX4), but light increases synthesis and AGPase activity, while starch breakdown to an early product, maltose, only occurs rapidly in the dark. Starch degradation occurs in several parallel pathways that may also be subject to light- or dark-specific regulation (some important factors are noted in gray). Starch synthesis and breakdown has been thoroughly reviewed (Ruan 2014, Stitt & Zeeman 2012, Streb & Zeeman 2012).

Figure 4.

Growth control systems in constant darkness and oscillating light–dark cycles. During etiolated growth (Left panel) the COP/DET/FUS complexes, together with the phytochrome-interacting factors (PIFs) promote hypocotyl growth, in part by repressing the photomorphogenesis-promoting factors such as hypocotyl 5 (HY5). The energy for the etiolated growth comes mainly from the seed reserves. During this stage, the influence of the etioplast is very limited, as it is not photosynthetically active. The clock runs weakly, but can be enhanced by added sugar. Clock cycling damps quickly due to lack of entraining stimuli and does not strongly regulate expression of output genes. During the day/night cycle (right panel), the chloroplasts have matured and, together with the clock, add additional control over hypocotyl growth. The clock is reset by light through photoreceptor proteins and via photosynthesis-derived sugars. It then begins to control genes involved in photosynthesis, carbon metabolism and growth, including at least two of the PIFs. The light to dark transition causes several acute signals: (1) photosynthesis stops and redox stress from photosystem activity is alleviated; (2) starch granules in the chloroplasts begin to break down to simpler sugars; (3) the clock protein TOC1 is destabilized in the dark in a ZTL-dependent process, relieving repression on the next phase of clock gene expression and on PIF activity; (4) PIF levels begin to increase because of less PHY activity, and fine-tune the timing and rate of hypocotyl growth.