The Phytochrome System and the Red/Far-Red Response

The phytochromes are a family of chromoproteins with a linear tetrapyrrole chromophore, similar to the ringed tetrapyrrole light-absorbing head group of chlorophyll. Phytochromes have two photo-interconvertible forms: Pr and Pfr. Pr absorbs red light (~667 nm) and is immediately converted to Pfr. Pfr absorbs far-red light (~730 nm) and is quickly converted back to Pr. Absorption of red or far-red light causes a massive change to the shape of the chromophore, altering the conformation and activity of the phytochrome protein to which it is bound. Pfr is the physiologically active form of the protein; therefore, exposure to red light yields physiological activity. Exposure to far-red light inhibits phytochrome activity. Together, the two forms represent the phytochrome system ((Figure)).

The phytochrome system acts as a biological light switch. It monitors the level, intensity, duration, and color of environmental light. The effect of red light is reversible by immediately shining far-red light on the sample, which converts the chromoprotein to the inactive Pr form. Additionally, Pfr can slowly revert to Pr in the dark, or break down over time. In all instances, the physiological response induced by red light is reversed. The active form of phytochrome (Pfr) can directly activate other molecules in the cytoplasm, or it can be trafficked to the nucleus, where it directly activates or represses specific gene expression.

Once the phytochrome system evolved, plants adapted it to serve a variety of needs. Unfiltered, full sunlight contains much more red light than far-red light. Because chlorophyll absorbs strongly in the red region of the visible spectrum, but not in the far-red region, any plant in the shade of another plant on the forest floor will be exposed to red-depleted, far-red-enriched light. The preponderance of far-red light converts phytochrome in the shaded leaves to the Pr (inactive) form, slowing growth. The nearest non-shaded (or even less-shaded) areas on the forest floor have more red light; leaves exposed to these areas sense the red light, which activates the Pfr form and induces growth. In short, plant shoots use the phytochrome system to grow away from shade and towards light. Because competition for light is so fierce in a dense plant community, the evolutionary advantages of the phytochrome system are obvious.

In seeds, the phytochrome system is not used to determine direction and quality of light (shaded versus unshaded). Instead, is it used merely to determine if there is any light at all. This is especially important in species with very small seeds, such as lettuce. Because of their size, lettuce seeds have few food reserves. Their seedlings cannot grow for long before they run out of fuel. If they germinated even a centimeter under the soil surface, the seedling would never make it into the sunlight and would die. In the dark, phytochrome is in the Pr (inactive form) and the seed will not germinate; it will only germinate if exposed to light at the surface of the soil. Upon exposure to light, Pr is converted to Pfr and germination proceeds.

Figure 1. The biologically inactive form of phytochrome (Pr) is converted to the biologically active form Pfr under illumination with red light. Far-red light and darkness convert the molecule back to the inactive form.

Plants also use the phytochrome system to sense the change of season. Photoperiodism is a biological response to the timing and duration of day and night. It controls flowering, setting of winter buds, and vegetative growth. Detection of seasonal changes is crucial to plant survival. Although temperature and light intensity influence plant growth, they are not reliable indicators of season because they may vary from one year to the next. Day length is a better indicator of the time of year.

As stated above, unfiltered sunlight is rich in red light but deficient in far-red light. Therefore, at dawn, all the phytochrome molecules in a leaf quickly convert to the active Pfr form, and remain in that form until sunset. In the dark, the Pfr form takes hours to slowly revert back to the Pr form. If the night is long (as in winter), all of the Pfr form reverts. If the night is short (as in summer), a considerable amount of Pfr may remain at sunrise. By sensing the Pr/Pfr ratio at dawn, a plant can determine the length of the day/night cycle. In addition, leaves retain that information for several days, allowing a comparison between the length of the previous night and the preceding several nights. Shorter nights indicate springtime to the plant; when the nights become longer, autumn is approaching. This information, along with sensing temperature and water availability, allows plants to determine the time of the year and adjust their physiology accordingly. Short-day (long-night) plants use this information to flower in the late summer and early fall, when nights exceed a critical length (often eight or fewer hours). Long-day (short-night) plants flower during the spring, when darkness is less than a critical length (often eight to 15 hours). Not all plants use the phytochrome system in this way. Flowering in day-neutral plants is not regulated by daylength.

The Blue Light Responses

Phototropism—the directional bending of a plant toward or away from a light source—is a response to blue wavelengths of light. Positive phototropism is growth towards a light source ((Figure)), while negative phototropism (also called skototropism) is growth away from light.

The aptly-named phototropins are protein-based receptors responsible for mediating the phototropic response. Like all plant photoreceptors, phototropins consist of a protein portion and a light-absorbing portion, called the chromophore. In phototropins, the chromophore is a covalently-bound molecule of flavin; hence, phototropins belong to a class of proteins called flavoproteins.

Other responses under the control of phototropins are leaf opening and closing, chloroplast movement, and the opening of stomata. However, of all responses controlled by phototropins, phototropism has been studied the longest and is the best understood.

In their 1880 treatise The Power of Movements in Plants, Charles Darwin and his son Francis first described phototropism as the bending of seedlings toward light. Darwin observed that light was perceived by the tip of the plant (the apical meristem), but that the response (bending) took place in a different part of the plant. They concluded that the signal had to travel from the apical meristem to the base of the plant.

Figure 2. Azure bluets (Houstonia caerulea) display a phototropic response by bending toward the light. (credit: Cory Zanker)

In 1913, Peter Boysen-Jensen demonstrated that a chemical signal produced in the plant tip was responsible for the bending at the base. He cut off the tip of a seedling, covered the cut section with a layer of gelatin, and then replaced the tip. The seedling bent toward the light when illuminated. However, when impermeable mica flakes were inserted between the tip and the cut base, the seedling did not bend. A refinement of the experiment showed that the signal traveled on the shaded side of the seedling. When the mica plate was inserted on the illuminated side, the plant did bend towards the light. Therefore, the chemical signal was a growth stimulant because the phototropic response involved faster cell elongation on the shaded side than on the illuminated side. We now know that as light passes through a plant stem, it is diffracted and generates phototropin activation across the stem. Most activation occurs on the lit side, causing the plant hormone indole acetic acid (IAA) to accumulate on the shaded side. Stem cells elongate under influence of IAA.

Cryptochromes are another class of blue-light absorbing photoreceptors that also contain a flavin-based chromophore. Cryptochromes set the plants’ 24-hour activity cycle, also know as its circadian rhythem, using blue light cues. There is some evidence that cryptochromes work together with phototropins to mediate the phototropic response.

Auxins

The term auxin is derived from the Greek word auxein, which means “to grow.” Auxins are the main hormones responsible for cell elongation in phototropism and gravitropism. They also control the differentiation of meristem into vascular tissue, and promote leaf development and arrangement. While many synthetic auxins are used as herbicides, IAA is the only naturally occurring auxin that shows physiological activity. Apical dominance—the inhibition of lateral bud formation—is triggered by auxins produced in the apical meristem. Flowering, fruit setting and ripening, and inhibition of abscission (leaf falling) are other plant responses under the direct or indirect control of auxins. Auxins also act as a relay for the effects of the blue light and red/far-red responses.

Commercial use of auxins is widespread in plant nurseries and for crop production. IAA is used as a rooting hormone to promote growth of adventitious roots on cuttings and detached leaves. Applying synthetic auxins to tomato plants in greenhouses promotes normal fruit development. Outdoor application of auxin promotes synchronization of fruit setting and dropping to coordinate the harvesting season. Fruits such as seedless cucumbers can be induced to set fruit by treating unfertilized plant flowers with auxins.

Cytokinins

The effect of cytokinins was first reported when it was found that adding the liquid endosperm of coconuts to developing plant embryos in culture stimulated their growth. The stimulating growth factor was found to be cytokinin, a hormone that promotes cytokinesis (cell division). Almost 200 naturally occurring or synthetic cytokinins are known to date. Cytokinins are most abundant in growing tissues, such as roots, embryos, and fruits, where cell division is occurring. Cytokinins are known to delay senescence in leaf tissues, promote mitosis, and stimulate differentiation of the meristem in shoots and roots. Many effects on plant development are under the influence of cytokinins, either in conjunction with auxin or another hormone. For example, apical dominance seems to result from a balance between auxins that inhibit lateral buds, and cytokinins that promote bushier growth.

Gibberellins

Gibberellins (GAs) are a group of about 125 closely related plant hormones that stimulate shoot elongation, seed germination, and fruit and flower maturation. GAs are synthesized in the root and stem apical meristems, young leaves, and seed embryos. In urban areas, GA antagonists are sometimes applied to trees under power lines to control growth and reduce the frequency of pruning.

GAs break dormancy (a state of inhibited growth and development) in the seeds of plants that require exposure to cold or light to germinate. Abscisic acid is a strong antagonist of GA action. Other effects of GAs include gender expression, seedless fruit development, and the delay of senescence in leaves and fruit. Seedless grapes are obtained through standard breeding methods and contain inconspicuous seeds that fail to develop. Because GAs are produced by the seeds, and because fruit development and stem elongation are under GA control, these varieties of grapes would normally produce small fruit in compact clusters. Maturing grapes are routinely treated with GA to promote larger fruit size, as well as looser bunches (longer stems), which reduces the instance of mildew infection ((Figure)).

Figure 3. In grapes, application of gibberellic acid increases the size of fruit and loosens clustering. (credit: Bob Nichols, USDA)

Abscisic Acid

The plant hormone abscisic acid (ABA) was first discovered as the agent that causes the abscission or dropping of cotton bolls. However, more recent studies indicate that ABA plays only a minor role in the abscission process. ABA accumulates as a response to stressful environmental conditions, such as dehydration, cold temperatures, or shortened day lengths. Its activity counters many of the growth-promoting effects of GAs and auxins. ABA inhibits stem elongation and induces dormancy in lateral buds.

ABA induces dormancy in seeds by blocking germination and promoting the synthesis of storage proteins. Plants adapted to temperate climates require a long period of cold temperature before seeds germinate. This mechanism protects young plants from sprouting too early during unseasonably warm weather in winter. As the hormone gradually breaks down over winter, the seed is released from dormancy and germinates when conditions are favorable in spring. Another effect of ABA is to promote the development of winter buds; it mediates the conversion of the apical meristem into a dormant bud. Low soil moisture causes an increase in ABA, which causes stomata to close, reducing water loss in winter buds.

Ethylene

Ethylene is associated with fruit ripening, flower wilting, and leaf fall. Ethylene is unusual because it is a volatile gas (C₂H₄). Hundreds of years ago, when gas street lamps were installed in city streets, trees that grew close to lamp posts developed twisted, thickened trunks and shed their leaves earlier than expected. These effects were caused by ethylene volatilizing from the lamps.

Aging tissues (especially senescing leaves) and nodes of stems produce ethylene. The best-known effect of the hormone, however, is the promotion of fruit ripening. Ethylene stimulates the conversion of starch and acids to sugars. Some people store unripe fruit, such as avocadoes, in a sealed paper bag to accelerate ripening; the gas released by the first fruit to mature will speed up the maturation of the remaining fruit. Ethylene also triggers leaf and fruit abscission, flower fading and dropping, and promotes germination in some cereals and sprouting of bulbs and potatoes.

Ethylene is widely used in agriculture. Commercial fruit growers control the timing of fruit ripening with application of the gas. Horticulturalists inhibit leaf dropping in ornamental plants by removing ethylene from greenhouses using fans and ventilation.

Nontraditional Hormones

Recent research has discovered a number of compounds that also influence plant development. Their roles are less understood than the effects of the major hormones described so far.

Jasmonates play a major role in defense responses to herbivory. Their levels increase when a plant is wounded by a predator, resulting in an increase in toxic secondary metabolites. They contribute to the production of volatile compounds that attract natural enemies of predators. For example, chewing of tomato plants by caterpillars leads to an increase in jasmonic acid levels, which in turn triggers the release of volatile compounds that attract predators of the pest.

Oligosaccharins also play a role in plant defense against bacterial and fungal infections. They act locally at the site of injury, and can also be transported to other tissues. Strigolactones promote seed germination in some species and inhibit lateral apical development in the absence of auxins. Strigolactones also play a role in the establishment of mycorrhizae, a mutualistic association of plant roots and fungi. Brassinosteroids are important to many developmental and physiological processes. Signals between these compounds and other hormones, notably auxin and GAs, amplifies their physiological effect. Apical dominance, seed germination, gravitropism, and resistance to freezing are all positively influenced by hormones. Root growth and fruit dropping are inhibited by steroids.