Phytochrome

Phytochromes are a class of photoreceptor proteins found in plants, bacteria and fungi. They respond to light in the red and far-red regions of the visible spectrum and can be classed as either Type I, which are activated by far-red light, or Type II that are activated by red light.^[2] Recent advances have suggested that phytochromes also act as temperature sensors, as warmer temperatures enhance their de-activation.^[3] All of these factors contribute to the plant's ability to germinate.

Phytochromes control many aspects of plant development. They regulate the germination of seeds (photoblasty), the synthesis of chlorophyll, the elongation of seedlings, the size, shape and number and movement of leaves and the timing of flowering in adult plants. Phytochromes are widely expressed across many tissues and developmental stages.^[2]

Other plant photoreceptors include cryptochromes and phototropins, which respond to blue and ultraviolet-A light and UVR8, which is sensitive to ultraviolet-B light.

Phytochromes consist of a protein, covalently linked to a light-sensing bilin chromophore.^[4] The protein part comprises two identical chains (A and B). Each chain has a PAS domain, GAF domain and PHY domain. Domain arrangements in plant, bacterial and fungal phytochromes are comparable, insofar as the three N-terminal domains are always PAS, GAF and PHY domains. However C-terminal domains are more divergent. 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.

Phytochromes are characterized by a red/far-red photochromicity. Photochromic pigments change their "color" (spectral absorbance properties) upon light absorption. In the case of phytochrome the ground state is P_r, 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 when viewed with white light. But once a red photon has been absorbed, the pigment undergoes a rapid conformational change to form the P_fr state. Here _fr indicates that now not red but far-red (also called "near infra-red"; 705–740 nm) is differentially absorbed. This shift in absorbance is apparent to the human eye as a slightly more greenish color. When P_fr absorbs far-red light it is converted back to P_r. Hence, red light makes P_fr, far-red light makes P_r. In plants at least P_fr is the physiologically active or "signalling" state.

The amplitude of phototropic curvature to blue light is enhanced by a prior exposure of seedlings to red light. This enhancement is mediated by phytochrome. ^[7] In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism. These reaction adjustments are also phytochrome-mediated. ^[8]

Phytochrome can also regulate the sensitivity of the gravitropic reaction.^[8]

Only some of the multiple phytochrome genes present in the plant genome participate in tropism regulation. ^[7][8]

Chemically, phytochrome consists of a chromophore, a single bilin molecule consisting of an open chain of four pyrrole rings, covalently bonded to the protein moiety via highly conserved cysteine amino acid. 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 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. Bilins are derived from the closed tetrapyrrole ring of haem by an oxidative reaction catalyzed by haem oxygenase, giving biliverdin, followed by reduction reactions. In the case of phytochromobilin, the final step is catalysed by phytochromobilin:ferredoxin oxidoreductase.^[9][10]

Chlorophyll and haem share a common precursor in the form of protoporphyrin IX, with its characteristic closed tetrapyrrole ring structure. In contrast to bilins, haem and chlorophyll carry a metal atom in the center of the ring, iron or magnesium, respectively.^[11]

The P_fr state 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 P_r form is localized there, the P_fr 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 P_fr form, may act as a kinase, and it has been demonstrated that phytochrome in the P_fr form can interact directly with transcription factors.^[12]

The phytochrome pigment was discovered by Sterling Hendricks and Harry Borthwick at the USDA-ARS Beltsville Agricultural Research Center in Maryland 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.

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 that more than one type of phytochrome existed; for example, the pea 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 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. Phytochrome 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 David Kehoe and Arthur Grossman at the Carnegie Institution at Stanford University identified the proteins, in the filamentous cyanobacterium Fremyella diplosiphon called RcaE with similarly to plant phytochrome that controlled a red-green photoreversible response called chromatic acclimation and identified a gene in the sequenced, published genome of the cyanobacterium Synechocystis with closer similarity to those of plant phytochrome. This was the first evidence of phytochromes outside the plant kingdom. Jon Hughes in Berlin and Clark Lagarias at UC Davis subsequently showed that this Synechocystis 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 a truncated Deinococcus phytochrome (PAS/GAF domains). This paper revealed that the protein chain forms a knot - a highly unusual structure for a protein. In 2008, two groups around Essen and Hughes in Germany and Yang and Moffat in the US published the three-dimensional structures of the entire photosensory domain. One structures was for the Synechocystis sp. (strain PCC 6803) phytochrome in Pr and the other one for the Pseudomonas aeruginosa phytochrome in the P_fr state. The structures showed that a conserved part of the PHY domain, the so-called PHY tongue, adopts different folds. In 2014 it was confirmed by Takala et al that the refolding occurs even for the same phytochrome (from Deinococcus) as a function of illumination conditions.

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 responses can be altered.^[13] 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.

In 2002, the light-induced interaction between a plant phytochrome and phytochrome-interacting factor (PIF) was used to control gene transcription in yeast. This was the first example of using photoproteins from another organism for controlling a biochemical pathway.^[14]

• Lia H, Zhangb J, Vierstra RD, Lia H (2010). "Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy". PNAS. 107 (24): 10872–10877. Bibcode:2010PNAS..10710872L. doi:10.1073/pnas.1001908107. PMC 2890762. PMID 20534495.
• "Tripping the Light Switch Fantastic", by Jim De Quattro, 1991.
• "Nature's Timekeeping", by Kit Smith, 2004.
• 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
• Gururani, Mayank Anand, Markkandan Ganesan, and Pill-Soon Song. "Photo-biotechnology as a tool to improve agronomic traits in crops." Biotechnology Advances (2014).