Phytochrome is a photoreceptor
Photoreceptor protein
Photoreceptors are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Some examples are rhodopsin in the photoreceptor cells of the vertebrate retina, phytochrome in plants, and bacteriorhodopsin and bacteriophytochromes in some bacteria...

, a pigment
A pigment is a material that changes the color of reflected or transmitted light as the result of wavelength-selective absorption. This physical process differs from fluorescence, phosphorescence, and other forms of luminescence, in which a material emits light.Many materials selectively absorb...

 that plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...

s use to detect light. It is sensitive to light in the red
Red is any of a number of similar colors evoked by light consisting predominantly of the longest wavelengths of light discernible by the human eye, in the wavelength range of roughly 630–740 nm. Longer wavelengths than this are called infrared , and cannot be seen by the naked eye...

 and far-red
Far-red light is light at the extreme red end of the visible spectrum, between red and infra-red light. Usually regarded as the region between 700 and 800 nm wavelength, it is dimly visible to some eyes. It is reflected or transmitted by plants because of the absorbance spectrum of...

 region of the visible spectrum
Visible spectrum
The visible spectrum is the portion of the electromagnetic spectrum that is visible to the human eye. Electromagnetic radiation in this range of wavelengths is called visible light or simply light. A typical human eye will respond to wavelengths from about 390 to 750 nm. In terms of...

. Many flowering plant
Flowering plant
The flowering plants , also known as Angiospermae or Magnoliophyta, are the most diverse group of land plants. Angiosperms are seed-producing plants like the gymnosperms and can be distinguished from the gymnosperms by a series of synapomorphies...

s use it to regulate the time of flowering based on the length of day and night (photoperiodism
Photoperiodism is the physiological reaction of organisms to the length of day or night. It occurs in plants and animals.Photoperiodism can also be defined as the developmental responses of plants to the relative lengths of the light and dark periods...

) and to set circadian rhythms. It also regulates other responses including the germination
Germination is the process in which a plant or fungus emerges from a seed or spore, respectively, and begins growth. The most common example of germination is the sprouting of a seedling from a seed of an angiosperm or gymnosperm. However the growth of a sporeling from a spore, for example the...

 of seeds
SEEDS is a voluntary organisation registered under the Societies Act of India....

 (photoblasty), elongation of seedlings, the size, shape and number of leaves
A leaf is an organ of a vascular plant, as defined in botanical terms, and in particular in plant morphology. Foliage is a mass noun that refers to leaves as a feature of plants....

, the synthesis of chlorophyll
Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...

, and the straightening of the epicotyl
In plant physiology, the epicotyl is the embryonic shoot above the cotyledons. In most plants the epicotyl will eventually develop into the leaves of the plant. In dicots, the hypocotyl is what appears to be the base stem under the spent withered cotyledons, and the shoot just above that is the...

 or hypocotyl
The hypocotyl is the stem of a germinating seedling, found below the cotyledons and above the radicle .-Dicots:...

 hook of dicot seedlings. It is found in the leaves of most plants.

Biochemically, phytochrome is a protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 with a bilin
Bilin (biochemistry)
Bilins, bilanes or bile pigments are biological pigments formed in many organisms as a metabolic product of certain porphyrins. Bilin was named as a bile pigment of mammals, but can also be found in lower vertebrates, invertebrates, as well as red algae, green plants and cyanobacteria...

A chromophore is the part of a molecule responsible for its color. The color arises when a molecule absorbs certain wavelengths of visible light and transmits or reflects others. The chromophore is a region in the molecule where the energy difference between two different molecular orbitals falls...


Phytochrome has been found in most plants including all higher plants; very similar molecules have been found in several bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

. A fragment of a bacterial phytochrome now has a solved three-dimensional protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...


Other plant photoreceptors include cryptochrome
Cryptochromes are a class of blue light-sensitive flavoproteins found in plants and animals. Cryptochromes are involved in the circadian rhythms of plants and animals, and in the sensing of magnetic fields in a number of species...

s and phototropin
Phototropins are photoreceptor proteins that mediate phototropism responses in higher plants. Along with cryptochromes and phytochromes they allow plants to respond and alter their growth in response to the light environment...

s, which are sensitive to light in the blue
Blue is a colour, the perception of which is evoked by light having a spectrum dominated by energy with a wavelength of roughly 440–490 nm. It is considered one of the additive primary colours. On the HSV Colour Wheel, the complement of blue is yellow; that is, a colour corresponding to an equal...

 and ultra-violet regions of the spectrum.


Phytochrome consists of two identical chains (A and B). Each chain has a PAS domain
PAS domain
The PAS domain is a protein domain contained in many signaling proteins where it functions as a signal sensor. PAS domains are found in a large number of organisms from bacteria to humans...

 and GAF domain
GAF domain
The GAF domain is a type of protein domain that is found in a wide range of proteins from all species.The GAF domain is named after some of the proteins it is found in: cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. The first structure of a GAF domain solved by Ho and colleagues...

. The PAS domain serves as a signal sensor and the GAF domain is responsible for binding to cGMP and also senses light signals. Together, these subunits form the phytochrome region, which regulates physiological changes in plants to changes in red and far red light conditions. In plants, red light changes phytochrome to its biologically active form, while far red light changes the protein to its biologically inactive form.

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.


Chemically, phytochrome consists of a chromophore
A chromophore is the part of a molecule responsible for its color. The color arises when a molecule absorbs certain wavelengths of visible light and transmits or reflects others. The chromophore is a region in the molecule where the energy difference between two different molecular orbitals falls...

, a single bilin molecule consisting of an open chain of four pyrrole
Pyrrole is a heterocyclic aromatic organic compound, a five-membered ring with the formula C4H4NH. It is a colourless volatile liquid that darkens readily upon exposure to air. Substituted derivatives are also called pyrroles, e.g., N-methylpyrrole, C4H4NCH3...

 rings, bonded to the protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 moiety. 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
Phycocyanobilin is a blue phycobilin, i.e., a tetrapyrrole chromophore found in cyanobacteria and in the chloroplasts of red algae, glaucophytes, and some cryptomonads. Phycocyanobilin is present only in the phycobiliproteins allophycocyanin and phycocyanin, of which it is the terminal acceptor of...

 (the chromophore of the phycobiliprotein
Phycobiliproteins are water-soluble proteins present in cyanobacteria and certain algae that capture light energy, which is then passed on to chlorophylls during photosynthesis. Phycobiliproteins are formed of a complex between proteins and covalently bound phycobilins that act as chromophores...

s used
by cyanobacteria and red algae
Red algae
The red algae are one of the oldest groups of eukaryotic algae, and also one of the largest, with about 5,000–6,000 species  of mostly multicellular, marine algae, including many notable seaweeds...

 to capture light for photosynthesis
Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...

) and to the bile
Bile or gall is a bitter-tasting, dark green to yellowish brown fluid, produced by the liver of most vertebrates, that aids the process of digestion of lipids in the small intestine. In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum...

 pigment bilirubin
Bilirubin is the yellow breakdown product of normal heme catabolism. Heme is found in hemoglobin, a principal component of red blood cells. Bilirubin is excreted in bile and urine, and elevated levels may indicate certain diseases...

 (whose structure is also affected by light exposure, a fact exploited in the phototherapy of jaundice
Jaundice is a yellowish pigmentation of the skin, the conjunctival membranes over the sclerae , and other mucous membranes caused by hyperbilirubinemia . This hyperbilirubinemia subsequently causes increased levels of bilirubin in the extracellular fluid...

d 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. Chlorophyll
Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...

 too 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 gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

 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
The cytosol or intracellular fluid is the liquid found inside cells, that is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondrion into compartments....

 and the Pr form is localized there, the Pfr form, when generated by light illumination, is translocated to the cell nucleus
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...

. 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
In chemistry and biochemistry, a kinase is a type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific substrates, a process referred to as phosphorylation. Kinases are part of the larger family of phosphotransferases...

, and it has been demonstrated that phytochrome in the Pfr form can interact directly with transcription factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...



The phytochrome pigment was discovered by Sterling Hendricks and Harry Borthwick at the USDA-ARS Beltsville Agricultural Research Center in Maryland
Maryland is a U.S. state located in the Mid Atlantic region of the United States, bordering Virginia, West Virginia, and the District of Columbia to its south and west; Pennsylvania to its north; and Delaware to its east...

 during a period from the late 1940s to the early 1960s. Using a spectrograph
A spectrograph is an instrument that separates an incoming wave into a frequency spectrum. There are several kinds of machines referred to as spectrographs, depending on the precise nature of the waves...

 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.

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 sequence was published by Howard Hershey and Peter Quail. By 1989, molecular genetics and work with monoclonal antibodies
Monoclonal antibodies
Monoclonal antibodies are monospecific antibodies that are the same because they are made by identical immune cells that are all clones of a unique parent cell....

 that more than one type of phytochrome existed; for example, the pea
A pea is most commonly the small spherical seed or the seed-pod of the pod fruit Pisum sativum. Each pod contains several peas. Peapods are botanically a fruit, since they contain seeds developed from the ovary of a flower. However, peas are considered to be a vegetable in cooking...

 plant 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 sequencing that Arabidopsis
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...

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
Maize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...

, 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. Phytohrome A or phyA is rapidly degraded in the Pfr form - much more so than the other members of the family. In the late 1980s, the Vierstra lab showed that phyA is degraded by the ubiquitin system, the first natural target of the system to be identified in eukaryotes.

In 1996 a gene in the newly sequenced genome of the cyanobacterium Synechocystis
Synechocystis sp. PCC6803 is a freshwater cyanobacterium capable of both phototrophic growth by oxygenic photosynthesis in sunlight and heterotrophic growth by glycolysis and oxidative phosphorylation during dark periods...

was noticed to have a weak similarity to those of plant phytochromes, the first evidence of phytochromes outside the plant kingdom. 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 prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

s including Deinococcus radiodurans
Deinococcus radiodurans
Deinococcus radiodurans is an extremophilic bacterium, one of the most radioresistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world's toughest bacterium in The Guinness Book Of World Records.-Name...

and Agrobacterium tumefaciens
Agrobacterium tumefaciens
Agrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of dicot. It is a rod shaped, Gram negative soil bacterium...

. 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 Deinococcus
The Deinococcus is the one genus of three of the Deinococcales group from the Deinococcus-Thermus phylum highly resistant to environmental hazards.There are 47 species of Deinococcus described according to NCBI on 25 august 2011 :...

phytochrome. This breakthrough paper revealed that the protein chain forms a knot - a highly unusual structure for a protein.

Genetic engineering

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 co-workers at Leicester University in England showed that by increasing the expression level of phytochrome A (which responds to far-red light), shade avoidance
Shade avoidance
Shade avoidance is a set of responses that plants display when they are subjected to the shade of another plant. It often includes elongation, altered flowering time, increased apical dominance and altered partitioning of resources...

 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.

Other sources

  • Hua Lia, Junrui Zhangb, Richard D. Vierstra, and Huilin Lia Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy PNAS
    Proceedings of the National Academy of Sciences
    The Proceedings of the National Academy of Sciences of the United States of America, usually referred to as PNAS, is the official journal of the United States National Academy of Sciences...

    June 1, 2010,
  • 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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