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Phytochrome is a photoreceptor, a pigment that plants use to detect light. It is sensitive to light in the red and far-red region of the visible spectrum. Many flowering plants use it to regulate the time of flowering based on the length of day and night (photoperiodism) and to set circadian rhythms. It also regulates other responses including the germination of seeds, elongation of seedlings, the size, shape and number of leaves, the synthesis of chlorophyll, and the straightening of the epicotyl or hypocotyl hook of dicot seedlings.
Biochemically, phytochrome is a protein with a bilin chromophore.
Phytochrome has been found in most plants including all higher plants; very similar molecules, now also called phytochromes, have been found in several bacteria. One bacterial phytochrome now has a solved three-dimensional protein structure.
Other plant photoreceptors include cryptochromes and phototropins, which are sensitive to light in the blue and ultra-violet regions of the spectrum.
Isoforms
There are two isoforms of phytochrome - Pr and Pfr. The Pr isoform absorbs red light (at 660nm) while the Pfr isoform absorbs far-red light (at 730nm). Absorption of light causes phytochrome to inter-convert. Hence, red light makes Pfr, far-red light makes Pr.
Phytochrome is made by the plant in the Pr form. Since daylight contains a lot of red light, during the day phytochrome is mostly converted to the Pfr form. At night, phytochrome will slowly convert back to the Pr form. Treatment with far-red light will also convert Pfr back to Pr. Since plants use red light for photosynthesis, and reflect and transmit far-red light, the shade of other plants also can make Pfr into Pr, triggering a response called shade avoidance.
In most plants, a suitable concentration of Pfr stimulates or inhibits physiological processes, such as those mentioned in the above examples. Thus Pfr is considered the active form of the pigment.
Biochemistry
Chemically, phytochrome consists of a chromophore, a single molecule with an open chain of four pyrrole rings, bonded to a protein. It is the chromophore that absorbs light, and as a result changes conformation, thereby also affecting the conformation of the attached protein, changing it from one isoform to the other.
The phytochrome chromophore is usually called phytochromobilin, and is closely related to phycobilin (the chromophore of the phycobiliproteins used by cyanobacteria and red algae to capture light for photosynthesis) and to the bile pigment bilirubin (whose structure is also affected by light exposure, a fact exploited in the phototherapy of jaundiced newborns). The term "bili" in all these names refers to bile. The structure of chlorophylls is slightly different: while they are also composed of four pyrroles, these are arranged in a ring and not in an open chain, and they contain a metal atom in the center.
The Pfr isoform passes on a signal to other biological systems in the cell, such as the mechanisms responsible for gene expression. Although this mechanism is almost certainly a biochemical process, it is still the subject of much debate. It is known that although phytochromes are synthesized in the cytosol and the Pr form is localized there, the Pfr form, when generated by light illumination, is translocated to the cell nucleus. This implies a role of phytochrome in controlling gene expression, and many genes are known to be regulated by phytochrome, but the exact mechanism has still to be fully discovered. It has been proposed that phytochrome, in the Pfr form, may act as a kinase, and it has been demonstrated that phytochrome in the Pfr form can interact directly with transcription factors.
Discovery
The phytochrome pigment was discovered by Sterling Hendricks and Harry Borthwick at the USDA-ARS in Beltsville, MD, during a period from the late 1940s to the early 1960s. Using a spectrograph built from borrowed and war-surplus parts, they discovered that red light was very effective for promoting germination or triggering flowering responses. The red light responses were reversible by far-red light, indicating the presence of a photoreversible pigment.
The phytochrome pigment was identified using a spectrophotometer in 1959 by biophysicist Warren Butler and biochemist Harold Siegelman. Butler was also responsible for the name, phytochrome, originally suggested as a joke. Before the existence of phytochrome was proven, skeptics called it “A pigment of the imagination.”
In 1983 the laboratories of Peter Quail and Clark Lagarias reported the chemical purification of the phytochrome molecule, and in 1987 the first phytochrome genetic sequence was published by Howard Hershey and Peter Quail. By 1989, it had been shown as a result of genetic sequencing and monoclonal antibody experiments that more than one type of phytochrome existed; for example the pea plant was shown to have at least two phytochromes. It is now known by genome sequencing that Arabidopsis has exactly five. However, although these phytochromes have different protein components, they all share the same chromophore.
In 1996 a gene in the newly sequenced genome of the cyanobacterium Synechocystis was noticed to have a weak similarity to plant phytochromes. Jon Hughes in Berlin and Clark Lagarias at UC Davis subsequently showed that this gene indeed encoded a bona fide phytochrome (named Cph1) in the sense that it is a red/far-red reversible chromoprotein. Presumably plant phytochromes are derived from an ancestral cyanobacterial phytochrome, perhaps by gene migration from the chloroplast to the nucleus. Subsequently phytochromes have been found in other prokaryotes including Deinococcus radiodurans and Agrobacterium tumefaciens. In Deinococcus phytochrome regulates the production of light-protective pigments, however in Synechocystis and Agrobacterium the biological function of these pigments is still unknown.
In 2005, the Viestra group at the University of Wisconsin published a three-dimensional structure of the photosensory domain of Deinococcus phytochrome. This breakthrough paper identified a highly unusual structure, a three-dimensional knot, in the structure of this unique protein.
Genetic engineering
Harry Smith, now at Nottingham University in England, and coworkers have shown that by increasing the expression level of phytochrome A (which responds to far-red light) shade avoidance responses can be altered. As a result, plants can expend less energy on growing as tall as possible and have more resources for growing seeds and expanding their root systems. This could have many practical benefits: for example, grass blades that would grow more slowly than regular grass would not require mowing as frequently, or crop plants might transfer more energy to the grain instead of growing taller.
References
- http://www.ars.usda.gov/is/timeline/light.htm
- http://www.mobot.org/jwcross/duckweed/phytochrome.htm#tetrapyrrole
- http://ucce.ucdavis.edu/files/filelibrary/616/17562.htm
- Terry and Gerry Audesirk. Biology: Life on Earth.
- Linda C Sage. Pigment of the imagination: a history of phytochrome research. Academic Press 1992. ISBN 0126144451
"Phytochrome"