Diversity among plants is wide and varied.  The genetic make up that is responsible for structural and functional variations is always dynamic.  Apart from interactions with its immediate cellular environment, it also interacts with the extracellular environment.  The three way interaction between the genetic material, cytoplasmic factor and external environmental factor sustains the life vibrant and dynamic.  The day, on which the life originated on this planet, it is subjected to the vagaries of nature.  In this struggle against nature, organisms have learnt to adopt by changing their functions and forms thus living beings progressed, during which process they accumulated more and more of informational materials and information material itself has undergone dramatic changes, yet it is still retaining the basic information genetic code.

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                                Phytochrome and the Circadian Clock



All in Good Time-Arabidopsis;


Biological time-keeping mechanisms have fascinated researchers since the movement of leaves with a daily rhythm was first described >270 years ago. The circadian clock confers a 24-hour rhythm on a range of processes including leaf movements and the expression of some genes. Molecular mechanisms and components underlying clock function have been described in recent years for several animal and prokaryotic organisms, and those of plants researcher are beginning to be characterize. The emerging model of the Arabidopsis clock has mechanistic parallels with the clocks of other model organisms, which consist of positive and negative feedback loops, but the molecular components appear to be unique to plants.



Living beings, during the course of millions of years of their structural existence on this planet have developed physiological systems which really respond to the changes in the environment with equal vigor and dynamicity.  Such regulated physiological processes which control growth and development exhibits a distinct pattern in their life cycle.  The behavioral pattern of them is well adapted to environmental factors like day period, dark period, temperature, water availability, nutrition, etc.  Like many animals, plants also show certain behavioral patterns, which again depends upon the changes in the environment.  Flowering, opening and closing of stomata, sleeping movements of leaves, opening and closing of petals, mitotic cycle are some of the examples of behavioral patterns exhibited by plants.


As man has adopted his sleeping habits to day and nights periods, plants also exhibit diurnal rhythm in closing and opening of stomata, folding and unfolding of leaflets, and flowers etc. The roe of K+H transporters in neurons of Hypothalamus has been implicated in human sleeping habits. 


The leaflets of Phaseolus multiflorus spread out horizontally during day and fold upwards at nights showing sleeping movements.  Such periodic movements are adapted to 24 hours cycle of day and night.  Such daily behavioral pattern of plants is called circadian rhythm (circa-about; dian-day). For example in Kalanchoe blossefeldiana the floral petals open during day period and close at nights.


The daily periodicity has a profound influence on the physiological properties of the plants, which manifest in their morphological changes.  Under such condition of the physiological processes, if there is a change or disturbance in the daily periodicity, plants still continue to behave in the same pattern, which means the circadian rhythm persists for sometime.  For example, if the seedlings of phaseolus multiflorus are grown under a photoperiodic cycle of 12 hours a day and 12 hours a night for a number of days, the leaves exhibit rhythmic circadian movements.  If such well adopted plants are transferred and maintained under continuous dark conditions, the opening and closing of leaves continue for a few cycles.  Later the rhythmic behavior peters off and ultimately vanishes as if it is exhausted


A similar behavioral pattern is found in the case of stomata in many plants and floral parts of Kalanchoe.  In phyllocactus, flowers open at night and close in the day times.  The above said behavioral pattern is attributed to the presence of an inbuilt time measuring devices and such a device is called Biological Clock.


The material basis for such a biological clock is known to by phytochrome. The chromophore protein complex by absorbing red light transforms into PfR form which slowly undergoes decay to PR form in dark.  The accumulation of PR and PfR forms in cells is known to perform many physiological activities within the cell(s).  Probably such pigments may act as allosteric modulators.  Changes in the concentration of PR or PfR form of pigments can affect the permeability properties of cell membranes and thus they can bring about turgour movements.  If a plant that is already adapted to a day length, if changed to different photoperiodic conditions, the existing active pigments still continue to operate for some time till they are completely exhausted or rendered inactive.  That is why when a plant which is exhibiting rhythmic behavior in particular periodic cycles is subjected to continuous dark conditions, the rhythmic movements persist and continues for few more cycles and then vanishes with time.


The circadian clocks of higher plants consist of many interacting genes – and the proteins that they code for – that together form a complex network. This complexity enables non-trivial responses to changes in the environment, for example if the timing of light and darkness is altered. In contrast with higher plants, the clock of the unicellular alga Ostreococcus tauri appears to be very simple, retaining little more than the core genes CCA1 and TOC1. These two genes are linked in a negative feedback loop, forming an oscillator that entrains to the light/dark cycles of the environment. A mathematical model of the clock, presented in paper [1], is able to capture the key features of the oscillations, including the timing of gene expression in light/dark cycles with different day length;


It has been thought that a complex response to the light requires multiple feedback loops between many clock genes, but in the study it was found that even a single loop can cause the non-trivial behavior observed in Ostreococcus. Key to this ability is the existence of multiple light inputs; light affects the rates of several biochemical reactions in the model, much like it does in the clocks of higher plants. An important question raised by the study concerns the relationship between light inputs and feedback loops: are these two alternative means of achieving a complex response, and if so what determines the balance between them?


The feedbacks between components in the circadian clock is usually thought to occur primarily at the level of genes (transcription), but it reveals that protein degradation exerts more powerful and direct control over the clock. Indiscriminate but temporary blocking of protein degradation halts the clock more abruptly and reliably than blocking protein production (transcription or translation). This has consequences for how clocks are studied in experiments; most measurements are made at the gene level, where important effects may be obscured and overlooked.


As a case in point, the paper shows that in the Ostreococcus clock, degradation of the CCA1 protein is under clock control, which means that a third, currently unidentified protein must also be a central player in the clock.


In many plants, the circadian clock is directly involved in vital decisions, for example about flowering time or cold resistance. The knowledge built up about the clocks of model organisms, including simple ones such as Ostreococcus tauri, will in the future allow researchers to better understand and control the clocks of commercially important crops and other plants, ultimately leading to increased yields to help feed the world’s growing population.






Dialy rhythm and biological clock


The operation of biological clock in photoperiodic plants has been explained by Bunning.  Accordingly, plants exhibit two phases of growth, i.e. photophilic phase (light loving) and scotophilic phase (dark loving).  But the physiological process that operates in such phases is not clearly explained.  However, Hyde proposed a theoretical model to explain the operation of biological clock. This is actually based on the relative concentrations of active and inactive phytochrome accumulated within the plant structures during photophilic period and scotophilic period.  Ultimately, it is the quantity of excited phytochrome that determines the rhythmic behavioral patterns and this is further believed to operate through allosteric modulations by active and inactive forms of phytochromes and other protein factors.


Pants use sugars to tell the time of day, according to research published in Nature today. Plants, like animals, have a 24 hour 'body-clock' known as the circadian rhythm. The ability to keep time provides an important competitive advantage and is vital in biological processes such as flowering, fragrance emission and leaf movement.


The structure of the Linear tetrapyrole shown above.  The pigment is attached to phytochrome protein through S-S linkage;


Rhythms that are repeated every 24 hours are collectively and specifically known as circadian rhythms. Flowering plants have internal timing mechanisms with a biochemical basis called biological clocks. Biological clocks trigger shifts in daily activity and help induce seasonal adjustments. Circadian rhythms are regular cycles of plant activities that occur on a twenty-four hour basis. For example, plants may fold their leaves into "sleep" positions even when kept in constant light or darkness. In some plants, leaves are extended out during the day, and held close to the stem at night. Such leaf movements occur even in constant light or darkness. Experiments have demonstrated that phytochrome plays a role.


Graphical abstract: Systems analyses of circadian networks

The circadian clock is a 24 hour timing device that co-ordinates biological activity with day/night cycles. The long history of systems analysis of circadian biology extends back to the first half of the last century when theoretical studies based on physiological experiments predicted the essential network properties, architecture and performance of circadian oscillators long before the first genetic components were isolated in the second half of the century. Systems approaches have continued to be important in analyzing the circadian network in the model plant Arabidopsis thaliana and in mammals. We describe how systems analyses of transcriptional changes have led to formal mathematical models of circadian oscillators. Predictions within these mathematical models have been used to identify potential new components of circadian systems. Cross-referencing circadian regulation of transcript abundance with transcriptomic responses to abiotic and biotic signals has increased understanding of the nature of circadian clocks and their significance in regulating the daily life of plants and animals. We also highlight the need for systems analyses of the circadianregulation of proteins, metabolites and other physiological activities such as ion channel regulation.

SDP plants flower when days length is short; ex. Poinsettia;

Image result for The microarray of expressed genes circadian Rhythm

Eight percent of all transcripts in macrophages are expressed with a circadian rhythm. (A) Phase-sorted heat map of genes transcribed in a circadian manner in peritoneal macrophages. Cells harvested via peritoneal lavage from four C57BL/6 mice every 4 h were magnetically purified for CD11b surface expression (see Fig. S5). Three individual RNA samples of each time were pooled and subjected to global gene transcription measurement by using Affymetrix chips. The analysis on circadian rhythmicity was done with CircWaveBatch. Lfdrs were determined and cutoff value was arbitrarily set to 0.1 as a measure for rhythmic versus nonrhythmic transcripts (see Fig. S7). Genes expressed in a circadian manner were plotted phase-sorted in a heat-map style (colors indicate min–max normalized relative expression: green, minimum expression; red, maximum expression). (B) Canonical clock gene expression in peritoneal macrophages. Individual datasets from A were plotted (filled circles) together with data obtained by a quantitative RT-PCR assay of the same samples (open circles, means ± SEM, n = 4, except for times CT 24 and 28, n = 3). Statistical analysis for qPCR data and chip data were performed with CircWave and CircWaveBatch, respectively (microarray: P ≤ 0.0001: Bmal1, Cry1, Per2; P ≤ 0.01: Rev-Erbα, Dbp, Cry2; P ≤ 0.05: Per1 and Clock; qPCR: P ≤ 0.0001: Bmal1, Cry1, Per1/2, Clock, Rev-Erbα, Dbp; P ≤ 0.001: Cry2).Circadian clock and gene expression during;