Experiments have shown that the phytochrome system is involved in the photoperiodic control of flowering. Experiments have found that only red light inhibits the flowering of short-day plants, and this inhibitory effect can be canceled out by following the red treatment with far-red light. Bearing in mind that far-red light reconverts P725 back into P665, it seems that a short-day plant will only flower if a sufficient proportion of its phytochrome is in the P665 form. The trigger to flowering could be either a high enough accumulation of P665 or a low enough concentration of P725. Current opinion favors the latter view, i.e P725 inhibits flowering and its conversion back to P665 removes the inhibition, thus allowing flowers to develop. In other words, flowering of short-day plants is promoted by the absence of P725 rather than the presence of P665.
In long-day plants the reverse seems to be true: accumulation of P725, resulting from long exposure to light, stimulates flowering.
How does phytochrome exert its effects on flowering? In the first place the photoperiodic stimulus is perceived by the leaves. This has been shown by covering a whole plant with a light-proof cover except for one leaf which is then subjected to light/dark treatment. Under these conditions the flowering response still takes place.
From the leaves the message is transmitted to the buds where flower formation is initiated. That the message takes the form of a hormone has been demonstrated by ingeniously grafting two short-day plants together. A plant which has been allowed to flower by exposure to short days is joined to another plant which has been prevented from flowering by being kept in long-day conditions. The result is that the latter blooms. The hormone that has been named as responsible for this is florigen, but so far it has not been isolated.
The molecular details of phytochrome signaling remain largely unknown. For example, it is not yet known how PPKs phosphorylate and regulate phyB or whether different protein kinases interact with this photoreceptor in the same way.
The Vierstra lab has published the three-dimensional structure of a Deinococcus phytochrome in its Pfr state. This reveals that the PAS domain forms a knot, a highly unusual structural motif for a protein.
Phytochrome is a photoreceptor that transmits signals that affect a variety of processes in plants. These include stomata opening and seed germination. It also regulates flowering and fruiting. Its signaling mechanisms are complex, involving a series of interactions between phytochrome and other proteins. Phytochrome is also found in algae and animals.
During light-dark cycles, phytochrome changes its state from Pr to Pfr and vice versa. It does this in response to a change in the ratio of red/far-red light that enters the leaf through the stomata. This mechanism is important for plants because it helps them adapt to changing light conditions. It is particularly crucial for plants that produce large numbers of small seeds. These seeds require a short period of exposure to red light (660 nm) for germination to begin. This process is called photoblastic germination. Phytochromes help to ensure that the right amount of light is available to initiate germination and maintain a steady state.
The phytochrome system is a complex molecular switch that is activated by a range of different light stimuli. It responds to both red and far-red light, and it is a very sensitive detector of red/far-red ratios. It has two reversible conformations, Pr and Pfr, which absorb red and far-red light, respectively. Its chromophore is a single bilin molecule, a chain of four pyrrole rings connected to a protein moiety via a cysteine amino acid. The protein moiety is attached to a redox-active cofactor, and its conformational changes are controlled by the binding of redox active compounds such as thiolate and nitrate.
Although most of the known phytochrome responses are based on experiments under artificial light conditions, which do not fully simulate natural light conditions. It is therefore important to conduct further experiments using more natural light conditions to understand the phytochrome system better.
The phylogenetic distribution of phytochrome-related coding sequences suggests that they are derived from cyanobacterial genes and have been expanded through gene transfer. However, phylogenetic trees that are based on the GAF domain have not been able to support strong hypotheses about their evolutionary origins. In addition, the structures of phytochrome proteins have proved resistant to crystallization and structural analysis. However, a series of protein-protein interaction studies has provided some insight into their functions.
As we have learned from our studies of photosynthesis, plants respond to many environmental cues in addition to the light-dark cycle. One of these is the length of the day, which is a key factor in plant development and in the seasonal onset of flowering. This phenomenon, known as photoperiodism, is regulated by a series of events involving phytochrome.
Phytochrome is a light-sensitive pigment that controls growth and development in all plants. It is the first plant hormone discovered and was isolated in 1959 at the Beltsville Agricultural Research Center by researchers from the USDA. Phytochrome enables plants to regulate many of their growth and development processes, including flowering and seed germination. It also plays a critical role in the directional response of plants to light, called phototropism. These responses are important for producing crops that grow in specific seasons or latitudes.
The first step in photoperiodic responses involves phytochrome signaling to the plant’s circadian clock, which is a cellular clock that is driven by a daily rhythm of protein turnover. The phytochrome-mediated pathway also includes a second messenger system that is influenced by temperature and can alter gene expression in response to a variety of external signals, such as the length of daylight.
During long days, Hd1 is converted from an activator to a repressor of Hd3a in a functional conversion that requires phytochrome light signaling (40, 45). This transformation depends on the amount of light and its duration, as well as the temperature. Interestingly, Hd1 activity is reduced by HOS1, which binds to CO in the presence of PfrB and inhibits the interaction of phytochrome with the repressor complex (46).
During the night, phytochrome inactivates itself through a process called dark reversion. The reversion reaction is slower than the activation reaction and depends on the temperature of the cell. In addition, a slow inactivation mechanism is triggered by a high concentration of cytosolic calcium. The two inactivation pathways compete for the same cytosolic calcium source, which is used to control the speed of dark reversion. The competing pathways are important because they ensure that the amount of active phytochrome remains consistent with the incoming light signal.
Seed germination is a complex process that is influenced by different environmental cues. The first step is the imbibition of water and the activation of seed cells, which must then decide whether to re-enter the cell cycle or remain arrested at the G2 phase. The activation of the cell cycle is important for the emergence of the coleorhiza and other organs. However, the emergence of these organs does not require the resumption of DNA replication, and the application of the cell cycle inhibitor hydroxyurea prevents coleorhiza formation in Brachypodium embryos. This suggests that cell division is not essential for germination.
The light-dependent initiation of seed germination is regulated by the phytochrome A (PhyA) and phyB receptors. These phytochromes are activated by red and far-red light, and they inhibit the repression of germination genes in the dark. In addition, the PhyA and PhyB receptors are also able to bind to a number of transcription factors, including the SOS proteins.
During germination, the cotyledons are enlarged and the plant becomes progressively photosynthetic. In Arabidopsis, the cotyledons are protected from the ambient environment by a thin sheath that contains the chloroplasts. This sheath is called the ligule and it has two layers, the inner one being called the epidermis, while the outer one is called the periclinal wall. The periclinal wall is responsible for the absorption of nutrients from the reserves and is controlled by a complex set of regulators, including the phytochrome signalling pathway.
The germination of seeds is a multistep process that involves the activation of the cotyledons and a series of cellular and biochemical events. In the beginning, a seed embryo undergoes a period of dormancy, and after it has imbibed water, the cotyledons elongate and develop chloroplasts. The cotyledons then become the primary site of photosynthesis. The physiology of seed germination is complex and depends on many different factors, including the type of light that the plant is exposed to and the duration of exposure.
To test the role of ERF55 and ERF58 in regulating the completion of seed germination, we sowed wild-type Col-0, erf55-1 erf58-2 double mutant, and two independent ERF58ox lines on 1/2x MS plates/1.5% agar and exposed them to W or phyA- and phyB-specific conditions. The final cumulative germination percentages were determined after 8 days of incubation.
Role of Phytochrome on Flowering in Plants
In plants, phytochromes act as a light sensor to trigger the response to the right type of light. These responses include germination, photoperiodism, and flowering. Phytochromes are also important for entraining the circadian clock and sensing the day length. In addition, phytochromes play a role in shade avoidance. Phytochromes are characterized by their red/far-red photochromic properties. In the ground state, phytochrome is a soluble, turquoise-blue pigment, but when exposed to red light, it undergoes a rapid conformational change to form the reversible Pfr state. This shift in absorbance to the far-red range allows the plant to respond to the appropriate light conditions.
The structure of phytochrome consists of two identical protein chains covalently linked to a bilin chromophore. The chromophore has a maximum absorbance around 650-670 nm. The protein parts of phytochrome are very similar to those of other photosensing proteins, including opsins and phototropins. They contain a PAS domain, GAF domain and a histidine kinase-like domain. The phytochrome structure is reminiscent of cyanobacterial phytochromes, suggesting that the proteins were derived from an ancestral cyanobacterium.
Several studies have shown that plants can adjust their growth rate and avoid seed dormancy through changes in phytochrome activity. For example, the synthesis of gibberellins can be triggered by phytochrome action. In addition, the elongation of stem-like structures can be prevented by phytochrome activity.
In addition to their role in regulating light-dependent responses, phytochromes also regulate gene expression. Phytochromes can bind to a small number of transcription factors and induce their activation. Moreover, they can protect these transcription factors from proteolytic degradation. These effects are mediated by the COP1 and SPA proteins.
Although most research on phytochrome signaling has been conducted using artificial light that is typically about 10 times lower than the natural sunlight, experiments in more natural conditions may reveal new roles for these photoreceptors. In particular, they may be important in interpreting the responses to temperature and light intensity that occur under natural conditions.
Interaction Of Phytochrome with Other Proteins
In addition to their direct regulatory roles, phytochromes can interact with other proteins and form heterodimers. For instance, phyB and phyC in Arabidopsis can form heterodimers that function to inhibit flowering during non-inductive photoperiods. In these conditions, the phyB-phyC heterodimer is more active than phyB alone. This may be because phyC is less thermally sensitive than phyB.