Phytochrome is a
photoreceptor, a pigmentthat plants use to detect light. It is sensitive to light in the redand far-redregion of the visible spectrum. Many flowering plants use it to regulate the time of floweringbased on the length of day and night ( photoperiodism) and to set circadian rhythms. It also regulates other responses including the germinationof seeds, elongation of seedlings, the size, shape and number of leaves, the synthesis of chlorophyll, and the straightening of the epicotylor hypocotylhook of dicotseedlings.
Biochemically, phytochrome is a
proteinwith a bilin chromophore.
Phytochrome has been found in most plants including all higher plants; very similar molecules have been found in several
bacteria. A fragment of a bacterial phytochrome now has a solved three-dimensional protein structure.
Other plant photoreceptors include
cryptochromes and phototropins, which are sensitive to light in the blueand ultra-violetregions of the spectrum.
Isoforms or states
Phytochromes are characterised by a red/far-red photochromicity. Photochromic pigments change their "colour" (spectral absorbance properties) upon light absorption. In the case of phytochrome the ground state is Pr, the r indicating that it absorbs red light particularly strongly. The absorbance maximum is a sharp peak 650–670 nm, so concentrated phytochrome solutions look turquoise-blue to the human eye. But once a red photon has been absorbed, the pigment undergoes a rapid conformational change to form the Pfr state. Here fr indicates that now not red but far-red (also called "near infra-red"; 705–740 nm) is preferentially absorbed. This shift in absorbance is apparent to the human eye as a slightly more greenish colour . When Pfr absorbs far-red light it is converted back to Pr. Hence, red light makes Pfr, far-red light makes Pr. In plants at least Pfr is the physiologically active or "signalling" state. Summary of the characteristics of plant phytochromes.
Chemically, phytochrome consists of a "
chromophore", a single bilin molecule consisting of an open chain of four pyrrolerings, bonded to the proteinmoiety. It is the chromophore that absorbs light, and as a result changes the conformation of bilin and subsequently that of the attached protein, changing it from one state or isoform to the other.
The phytochrome chromophore is usually phytochromobilin, and is closely related to
phycocyanobilin(the chromophore of the phycobiliproteins used by cyanobacteriaand red algaeto capture light for photosynthesis) and to the bilepigment bilirubin(whose structure is also affected by light exposure, a fact exploited in the phototherapyof jaundiced newborns).The term "bili" in all these names refers to bile. Bilins are derived from the closed tetrapyrrole ring of haem by an oxidative reaction catalysed by haem oxygenase to yield their characteristic open chain. Chlorophylltoo is derived from haem. In contrast to bilins, haem and chlorophyll carry a metal atom in the center of the ring, iron or magnesium, respectively.
The Pfr state passes on a signal to other biological systems in the cell, such as the mechanisms responsible for
geneexpression. Although this mechanism is almost certainly a biochemicalprocess, it is still the subject of much debate. It is known that although phytochromes are synthesized in the cytosoland 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.
The phytochrome pigment was discovered by
Sterling Hendricksand Harry Borthwickat the USDA-ARS Beltsville Agricultural Research Centerin Marylandduring a period from the late 1940s to the early 1960s. Using a spectrographbuilt 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
spectrophotometerin 1959 by biophysicist Warren Butlerand biochemist Harold Siegelman. Butler was also responsible for the name, phytochrome.
In 1983 the laboratories of Peter Quail and Clark Lagarias reported the chemical purification of the intact phytochrome molecule, and in 1985 the first phytochrome
gene sequencewas published by Howard Hershey and Peter Quail. By 1989, molecular genetics and work with monoclonal antibodiesthat more than one type of phytochrome existed; for example, the peaplant was shown to have at least two phytochrome types (then called type I (found predominantly in dark-grown seedlings) and type II (predominant in green plants)). It is now known by genome sequencingthat Arabidopsis has five phytochrome genes (PHYA - E) but that rice has only three (PHYA - C). While this probably represents the condition in several di- and monocotyledonous plants, many plants are polyploid. Hence maize, for example, has six phytochromes - phyA1, phyA2, phyB1, phyB2, phyC1 and phyC2. While all these phytochromes have significantly different protein components, they all use phytochromobilin as their light-absorbing chromophore. In the late 1980s, the Vierstra lab showed that phyA is degraded by the ubiquitin system, the first identified natural target of the system to be identified in eukaryotes.
In 1996 a gene in the newly sequenced genome of the cyanobacterium "
Synechocystis" was noticed to have a weak similarity to those of 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 Vierstra and Forest labs at the University of Wisconsin published a three-dimensional structure of the photosensory domain of
Deinococcusphytochrome. This breakthrough paper revealed that the protein chain forms a knot - a highly unusual structure for a protein.
Around 1989 several laboratories were successful in producing ("
transgenic plants") which produced elevated amounts of different phytochromes (" overexpression"). In all cases the resulting plants had conspicuously short stems and dark green leaves. Harry Smith and coworkers at Leicester University in England showed that by increasing the expression level of phytochrome A (which responds to far-red light) shade avoidanceresponses 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.
* Terry and Gerry Audesirk. "Biology: Life on Earth."
* Linda C Sage. "A pigment of the imagination: a history of phytochrome research." Academic Press 1992. ISBN 0-12-614445-1
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