Phytochrome Signalling: How Plants Perceive Red and Far-Red Light

A detailed examination of phytochrome photoreceptors — Pr/Pfr interconversion, shade avoidance syndrome, seed germination cues, and the molecular cascade...

What Are Phytochromes?

Phytochromes are biliprotein photoreceptors that sense red (R, ~660 nm) and far-red (FR, ~730 nm) light. They exist in two photo-interconvertible forms: Pr (red-absorbing) and Pfr (far-red-absorbing). Pr absorbs red light and converts to Pfr; Pfr absorbs far-red light and converts back to Pr. In darkness, Pfr slowly reverts to Pr through a thermally driven process called dark reversion.

This seemingly simple bistable switch underpins some of plants' most sophisticated behaviours: germination timing, shade avoidance, flowering control, and neighbour detection.

The Phytochrome Gene Family

Arabidopsis has five phytochrome genes (PHYA–PHYE), each encoding a ~120 kDa apoprotein that autocatalytically attaches a phytochromobilin chromophore. The holoprotein assembles as a homodimer:

| Phytochrome | Stability in Light | Role |

|---|---|---|

| phyA | Labile (degraded in light) | Very-low-fluence responses; germination, de-etiolation in persistent dark |

| phyB | Light-stable | Red/far-red ratio sensing; shade avoidance, flowering, circadian entrainment |

| phyC–phYE | Light-stable | Redundant and modulatory roles; phyC affects flowering; phyD acts with phyB |

phyA dominates during seedling emergence from soil (etiolation); as the seedling encounters light, phyA is rapidly degraded and phyB takes over as the primary shade detector.

Photomorphogenesis: The Phytochrome-Mediated Transition

When a dark-grown (etiolated) seedling encounters light, phyB (initially in Pr form) converts to Pfr, triggering a massive transcriptional reprogramming — the transition from skotomorphogenesis (dark development) to photomorphogenesis (light development):

  • Inhibition of hypocotyl elongation. Pfr activates HY5, a bZIP transcription factor that upregulates photomorphogenesis genes and represses auxin-mediated elongation.
  • Chloroplast development. Pfr promotes expression of CAB (chlorophyll a/b binding) genes, RuBisCO small subunit, and other photosynthesis components.
  • Cotyledon expansion. Cell expansion in cotyledons is promoted via cytokinin signalling downstream of Pfr.
  • Anthocyanin synthesis. Pfr activates the MYB-bHLH-WD40 complex, driving anthocyanin production for UV protection.

In the cop/det/fus mutants (constitutive photomorphogenic), seedlings undergo photomorphogenesis even in darkness — these genes encode repressors that are inactivated by Pfr. The COP9 signalosome is a proteasome-related complex that targets HY5 for degradation in darkness; Pfr inhibits this complex, stabilising HY5.

Shade Avoidance Syndrome

The shade avoidance response is perhaps the most ecologically significant phytochrome-mediated behaviour. In dense vegetation, the red:far-red ratio (R:FR) drops from ~1.2 in full sunlight to ~0.1–0.3 under a leaf canopy, because chlorophyll absorbs red light strongly while transmitting and reflecting far-red.

phyB in Pfr form (which accumulates under high R:FR) represses shade-avoidance genes. When R:FR drops, Pfr converts to Pr, the repressive signal lifts, and a transcriptional cascade — driven primarily by PIF (PHYTOCHROME-INTERACTING FACTOR) transcription factors — activates elongation growth:

  • Hypocotyl and stem elongation via upregulation of auxin biosynthesis (YUCCA genes) and auxin transport (PIN genes).
  • Petiole elongation and hyponasty (upward leaf movement) to project leaves above competitors.
  • Accelerated flowering via upregulation of FT (FLOWERING LOCUS T), enabling reproduction before resources are exhausted.
  • Reduced branching and leaf thickness. Resources are diverted from lateral branches and leaf mesophyll toward internode elongation.

PIFs (PIF4, PIF5, PIF7) are bHLH transcription factors that are stable in darkness (or low R:FR) but phosphorylated and degraded via the ubiquitin-proteasome pathway when they interact with Pfr. Shade conditions reduce Pfr, stabilise PIFs, and trigger the elongation programme.

Seed Germination: The Phytochrome Switch

Many seeds require a light stimulus to germinate — a mechanism that ensures they are close enough to the soil surface for seedling survival. The germination response is typically a low-fluence response (LFR) mediated by phyB:

  1. A brief pulse of red light converts Pr → Pfr in the seed.
  2. Pfr migrates to the nucleus and activates transcription of HY5 and other germination-promoting genes.
  3. A subsequent pulse of far-red light converts Pfr → Pr, reversing the germination signal (the "red/far-red reversibility" test, which demonstrates phytochrome involvement).

Some seeds (e.g., lettuce, Arabidopsis) have a very-low-fluence response (VLFR) mediated by phyA, which can be triggered by extremely brief light exposure during soil disturbance.

Phytochrome and the Circadian Clock

phyB contributes to circadian entrainment — the process by which the endogenous ~24-hour clock is set to match the external day-night cycle. Under light-dark cycles, Pfr peaks at dawn (after a night of dark reversion), providing a synchronising pulse to the circadian oscillator (CCA1/LHY and TOC1). Mutations in PHYB lengthen the free-running period of the circadian clock and reduce the amplitude of clock gene oscillations.

Practical Implications for Indoor Plants

  • Window orientation matters more than you think. A south-facing window (Northern Hemisphere) provides high R:FR and moderate FR. A north-facing window is lower in total light but still has a high R:FR ratio. Plants near a window receive direct light; those deeper in the room receive reflected light that is enriched in FR (because walls and furniture absorb red preferentially), potentially triggering shade avoidance.
  • Leggy, etiolated growth is not just "not enough light." It is a specific phyB-mediated shade-avoidance response. The plant senses low R:FR, stabilises PIFs, and reallocates carbon to internode elongation at the expense of leaf expansion.
  • Red LEDs for seed starting. Red-rich grow lights (660 nm peak) efficiently convert phyB to Pfr, promoting compact, photomorphogenic growth. Far-red supplementation (730 nm) can be used strategically to induce flowering in short-day plants but should be avoided for leafy growth.

Summary Table

| Response | Primary Phytochrome | R:FR Condition | Outcome |

|---|---|---|---|

| Shade avoidance | phyB | Low R:FR (< 0.5) | Stem elongation, hyponasty |

| Seed germination | phyB (LFR), phyA (VLFR) | High R:FR (> 1.0) | Germination triggered |

| De-etiolation | phyB (high fluence), phyA (VLFR) | Light → Pfr | Inhibited elongation, green development |

| Circadian entrainment | phyB | Dawn (Pfr peak) | Clock synchronised |

| Flowering acceleration | phyB low Pfr + PIF → FT | Low R:FR | Early flowering (shade escape) |

Quick-Reference Care Tip

If your plant is stretching toward the window with long internodes and sparse leaves, it is not just light-deprived — it is actively sensing shade via phyB. Increase light intensity and, if using grow lights, ensure they include a strong red component (660 nm) to keep phyB in the active Pfr form.

Identify lighting problems and get tailored care plans — Plant Identifier.

Identify your plant with Green Sage →