Plants can sense light direction, quality (wavelength), intensity and periodicity. Light induces phototropism, photomorphogenesis, chloroplast differentiation and various other responses such as flowering and germination.

Light quality is mainly sensed by the presence of different light receptors specific for different wavelengths. The red/far red photoreceptors are called phytochrome. There are at least 2 classes of blue light receptors; cryptochrome recognizes blue, green and UV-A light, while phototropin perceives blue light.


Analysis of Photomorphogenesis

Plants exhibit different growth habits in dark and light. In the dark they have elongated stems, undifferentiated chloroplasts and unexpanded leaves. This is called skotomorphogenesis. Photomorphogenesis (light grown) involves the inhibition of stem elongation, the differentiation of chloroplasts and accumulation of chlorophyll, and the expansion of leaves. Thus the same stimulus causes opposite effects on cell elongation in leaves and stems. Photomorphogenesis can be induced by red, far red and blue light.

Much of our knowledge of light perception and signaling has come from genetic analyses of photomorphogenesis. Essentially two types of mutant screens have been performed:

  1. Screens for mutants that look dark grown even in the light (ie. insensitive or unresponsive to light). These are often designated as hy mutants for hypocotyl elongated, a dark grown character. These mutants have identified the known light receptors and a couple other genes that function as positive regulators of the light responses.
  2. Screens for mutants that look light grown even in the dark. These are designated as cop for constitutive photomorphogenic or det for de-etiolated (etiolated is a term used to describe the dark grown habit). These recessive mutants are epistatic to hy mutants indicating that they function as negative regulators of signal transduction steps downstream of the receptors. In other words, because loss of function mutations allow photomorphogenic development in the absence of the inducing signal (light), the normal function of the DET and COP genes is to repress photomorphogenesis in the dark.



Phytochrome is a protein containing a covalently attached chromophore. Phytochrome exists in 2 interconvertable conformations with different absorbtion spectra. Pfr absorbs far red and is generally the biologically active conformation. Pr absorbs red. Absorbtion of red light converts Pr to Pfr while absorbtion of far red converts Pfr to Pr. Phytochrome responses are classically defined by their red/far red reversibility. For example, lettuce seeds require light to germinate. Red light induces germination but if followed by a pulse of far red light, germination is inhibited. It also contains a domain resembling a protein kinase and has been shown to autophosphorylate, however the functional significance of this in light signal transduction is unknown.

Phytochrome can measure light quality because if light contains more red than far red light (as is the case in daytime sunlight), most phytochrome will be in the Pfr form. Phytochrome mediates a variety of photomorphogenic phenomena including leaf expansion and inhibition of stem elongation. One classic example is in the shade avoidance response of shade intolerant plants. Foliage readily absorbs red light and so in the shade of another plant there is higher amounts of far red light which will drive phytochrome to the Pr form. Pr does not inhibit stem elongation which allows shaded plants to elongate and grow to reach the sunlight.

Arabidopsis contains 5 phytochrome genes, PHYA-E, each with distinct but often overlapping functions. PHYA is photolabile while PHYB is light stable. Different phytochromes control different plant processes in response to different intensities of light. Responses are classified as hi-irradiance (HI), low fluence (LF) or very low fluence (VLF) based on the intensity of light required to trigger the response. Phytochrome studies are further complicated by the fact that different species show different sets of responses to given light conditions. Therefore it is difficult to draw generalizations about the functions of different phytochromes.

In the dark, phytochrome is localized to the cytoplasm. In the light, phytochrome translocates to the nucleus. Phytochrome physically interacts with at least one transcription factor, PIF3, in a light dependent manner. PIF3 is required for phytochrome mediated photomorphogenesis because antisense lines show elongated hypocotyls in the light (ie. decreased light response). PIF3 binds to G-BOX elements of light regulated genes and is required for phytochrome mediated regulation of several genes.



Blue, green and UVA light are all perceived by a receptor called cryptochrome. It is a flavin protein with 2 chromophores attached, one for green, one for blue. There are 2 cryptochrome genes in arabidopsis, CRY1 and 2. Again, they have distinct but overlapping functions. hy4/cry1 is a nonphotomorphogenic mutant defective for the blue light receptor. CRY proteins appear constitutively nuclear, although there are indications that there may be some CRY functions in the cytoplasm too.

Cryptochrome action requires the presence of phytochrome because some phytochrome mutants are non-photomorphogenic in blue or green light. However the cryptochrome mutant is photomorphogenic in red light (with far red reversibility) indicating that phytochrome action does not require cryptochrome. Evidence suggests that phytochrome and cryptochrome physically interact. CRY protein can be phosphorylated in vitro by the protein kinase activity of PHY-A. Furthermore, PHYB and CRY2 interact in plant extracts and exhibit FRET in plant cells (Mas et al., 2000). CRY1 and 2 also appear to directly interact with COP1, a factor involved in the negative regulation of photomorphogenesis in the dark (see below) (Yang et al., 2001).



HY5 is a transcription factor that is a key regulator of photomorphogenesis in both the phy and cry pathways. hy5 mutants show a dark grown habit in the light indicating that HY5 is required for light response. In the light, the level of HY5 protein increases and in the dark, it declines. HY5 mRNA increases in response to phytochrome activation but the gene does not have a G-BOX suggesting it may not be regulated by PIF3.


COP1 and the COP9 Signalsome

A large number of mutants were identified with constitutive photomorphogenesis (cop) or de-etiolated (det) phenotypes. These mutants look light grown in the dark and therefore are thought to function as negative regulators of light signal transduction pathways (ie. the signal transduction pathways are active in the absence of light). Many of these mutants encode proteins that form a large complex called the COP9 signalsome (CNS). The CNS is a nuclear complex that is similar to the 26S proteosome. This is a proteolytic complex that degrades ubiquitinated proteins.

COP1 is another protein that inhibits photomorphogenesis. In the dark, COP1 is present in the nucleus, but in the light it is only found in the cytoplasm. COP1 contains a ring-finger, which is a feature of many E3 ubiquitin ligases, which are involved in targeting proteins for 26S proteosome-mediated degredation. COP1 interacts with HY5, and in the dark HY5 protein levels show a decline that is dependent on COP1 and CNS. Thus it is hypothesized that in the dark, COP1 targets HY5 for degredation by CNS.

As mentioned, CRY1 and 2 are constitutively nuclear and also interact with COP1. It is hypothesized that CRY binding inhibits COP1 activity. Another factor that functions in phytochrome signal transduction, SPA1, also interacts with COP1. Thus, all photomorphogenetic signal transduction pathways appear to converge on COP1. Inhibition of COP1 may then allow accumulation of HY5 and the response to light.



Several plant hormones are thought to be involved in photomorphogenesis. Pfr appears to inhibit the sensitivity of hypocotyls to GA, thus in the dark when Pfr is depleted, the hypocotyls become more sensitive to GA and elongate. However brassinolide has a much more central role in photomorphogenesis. Several of the cop and det mutants are rescuable with exogenous brassinolide (ie. they show dark grown habit in the dark). The det2 mutant of arabidopsis was cloned and has sequence homology with mammalian steroid 5a-reductase. This suggests a function of the DET2 gene product in a particular step of brassinolide biosynthesis. Similarly, the CPD gene shows a cop-like mutant phenotype, was cloned and has sequence similarity to another enzyme in testosterone biosynthesis, suggesting it functions in another step of the brassinolide pathway. Rescue experiments with pathway intermediates were consistent with the proposed functions of these genes. Thus, light appears to control photomorphogenesis by downregulating brassinolide production.



Another blue light receptor is called phototropin. Arabidopsis contains 2 phototropins. These are involved in phototropism, but not photomorphogensis (hypocotyl elongation).

Phototropism is the directional growth in response to directional light. Shoots are positively phototropic (grow toward light) while roots often show negative phototropism (grow away from light). Directional light causes a redistribution of auxin in shoot tissues such that the side away from the light accumulates higher levels and grows faster, causing bending toward the light. Phototropism is controlled mainly by blue/UVA light. However the receptor is different from cryptochrome because the cry mutants are still phototropic. A mutant identified as nonphototropic hypocotyl1 (nph1), acts at the level of light perception in the phototropic response but still retains normal photomorphogenetic responses. This gene was recently renamed PHOTOTROPIN1 (PHOT1). Arabidopsis contains two phototropin genes, PHOT1 and PHOT2. PHOT protein is another flavoprotein containing 2 flavin mononucleotide chromophores. The protein also contains a protein kinase domain and blue light induces PHOT kinase activity.




Quail, P. H. (2002). Photosensory perception and signalling in plant cells: new paradigms? Curr. Opin. Cell Biol. 14, 180188.

Mas, P., Devlin, P. F., Panda, S., and Kay, S. A. (2000). Functional interaction of phytochrome B and cryptochrome 2. Nature 408, 207-11.

Yang, H.-Q., Tang, R.-H., and Cashmore, A. R. (2001). The Signaling Mechanism of Arabidopsis CRY1 Involves Direct Interaction with COP1. Plant Cell 13, 2573-2587.