CIRCADIAN RHYTHM & BIOLOGICAL CLOCK

 

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.

 

Plant Physiol

All in Good Time-Arabidopsis; www.cell.com

 

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 are beginning to be characterized. 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 and 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. to.  For example in Kalanchoe blossefeldiana the floral petals open during day period and close at nights.

 

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).

 

The daily periodicity has a profound influence on the physiological properties of the plant, 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.

 

http://www.hfsp.org/

 

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 daylength.

 

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 paper [2] 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. http://www.hfsp.org/

 

 

 

 

 

Dialy rhythm and biological clock

www.phys.org

 

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. http://www.sciencedaily.com/

 

https://smartsite.ucdavis.edu

 

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. https://smartsite.ucdavis.edu

 

Graphical abstract: Systems analyses of circadian networks

http://pubs.rsc.org/

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. http://pubs.rsc.org/

 

 

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Flow diagram of postulated regulatory network involved in the generation of circadian regulation of metabolism and behavior at the cellular level. The regulatory loops generate a circadian rhythm in energy transduction, resulting in cycles of redox and phosphorylation potential, and a rhythmic membrane potential, which controls circadian rhythmic changes in sensitivity of membrane bound photoreceptors. In addition, and more generally, membrane-bound (e.g. two-component) signal transduction systems not only synchronize the circadian rhythm in energy transduction with the daily light-dark cycle via several photoreceptor systems, but also modulate metabolic control of timing by many other environmental signals or parameters of state. Redox and phosphorylation potential gate the input of transcription factors to an autoregulatory cycling of transcription and translation, protein synthesis and turnover. This is the basis for the evolution of latitudinal ecotypes of Chenopodium rubrum with specific period lengths for their circadian rhythms and the division of the circadian cycle in a photophile- and scotophile-element that is specific for photoperiodic control. By scanning the seasonal changes in the daily light-dark cycle for coincidence with the ecotype specific scotophile-photophile pattern, the critical photoperiod switches the system from vegetative to reproductive development.

   Irrespective of the flexibility of plants in modifying their photoperiodic behavior in adapting to specific environmental conditions as just mentioned, the following essentials of the photoperiodic reaction have to be kept in mind as a basis for further considerations:

(a) Short-day (SDP) and long-day plants (LDP) show opposite reactions to a given photoperiod.

(b) Reactionss result from coincidence or non-coincidence of light and dark phases of the photoperiod with corresponding phases of an endogenous circadian rhythm and the main photoreceptors are the plant sensory pigment systems phytochrome and cryptochrome. Circadian rhythm and photoreceptors have the same properties in SDP and LDP.

(c) Critical photoperiodic induction produces irreversible changes in the leaves of SDP and LDP leading to a common state both in SDP and LDP, as proven by grafting experiments. There is no difference between SDP and LDP in their response towards a common inductor from a grafted leaf from an induced short- or long-day plant.

The integration of activity of Chenopodium plants on a hydraulic-electrochemical level is expressed by a diurnal rhythm in the resting membrane potential measured with contact electrodes. The membrane state could be gated by the energy state of cells. From earlier studies we compiled evidence in favor of a circadian rhythm in overall energy transduction producing a circadian rhythm in energy charge and redox state (NADPH2/NADP). The ratio of metabolic coupling nucleotides would be relatively temperature independent and thus could fulfil the requirements for precise temperature-compensated time-keeping. The phytochrome photoreceptors, involved in photoperiodic control of development, could via changes in pyridine nucleotide pool sizes and changes in nucleotide ratios regulate transcription-translational loops by redox and phosphorylation controlled transcription factors.

 

 

Math Model For Circadian Rhythm Created

ScienceDaily (Aug. 30, 2007) — The internal clock in living beings that regulates sleeping and waking patterns -- usually called the circadian clock -- has often befuddled scientists due to its mysterious time delays. Molecular interactions that regulate the circadian clock happen within milliseconds, yet the body clock resets about every 24 hours. What, then, stretches the expression of the clock over such a relatively long period?

 

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Cornell researchers have contributed to the answer, thanks to new mathematical models recently published.

In the August online edition of Public Library of Science (PLOS) Computational Biology, Cornell biomolecular engineer Kelvin Lee, in collaboration with graduate student Robert S. Kuczenski, Kevin C. Hong '05 and Jordi Garcia-Ojalvo of Universitat Politecnica de Catalunya, Spain, hypothesize that the accepted model of circadian rhythmicity may be missing a key link, based on a mathematical model of what happens during the sleeping/waking cycle in fruit flies.

"We didn't discover any new proteins or genes," Lee said. "We took all the existing knowledge, and we tried to organize it."

Using mathematical models initially created by Hong, who has since graduated, the team set out to map the molecular interactions of proteins called period and timeless -- widely known to be related to the circadian clock.

The group hypothesized that an extra, unknown protein would need to be inserted into the cycle with period and timeless, a molecule that Kuczenski named the focus-binding mediator, in order for the cycle to stretch to 24 hours.

Lee said many scientists are interested in studying the circadian clock, and not just to understand such concepts as jet lag -- fatigue induced by traveling across time zones. Understanding the body's biological cycle might, for example, lead to better timing of delivering chemotherapy, when the body would be most receptive, Lee said.

 

Adapted from materials provided by Cornell University.

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A graphic representation of the molecular interactions of circadian rhythm, based on work recently published by Cornell researchers. They proposed that a new, unknown molecule, called the focus-binding mediator (FBM) would need to be inserted into the cycle along with proteins period and timeless, in order for mathematical modeling of the system to make sense. (Credit: Image courtesy of Cornell University)

 

 Circadian rhythms, biological rhythms with a period of approximately 24 hours, appear to evolve from the adaptation of life to light/dark and temperature cycles on the Earth. Circadian rhythms have been observed among major phyla, from cyanobacteria, algae, fungi, plants, to animals, including insects, vertebrates such as fish, mouse, humans. Circadian rhythms appear be controlled by a self-sustained and autonomous clock. Conceptually, the circadian clock has three components as shown in the figure below:

 

Plant Physiol

 
The first one is an input pathway that links the internal cycle to external light-dark (and maybe temperature) cycles through photic or non-photic signal transduction pathways, which is largely unknown, but through which it is believed that the clock can be synchronized. The second is an autonomous, self-sustained and endogenous pacemaker or oscillator, which generates the circadian oscillations. The final one is an output pathway, which relays the circadian rhythmicity to overt physiological and behavioral rhythms. The process is also largely unknown. In other words, circadian clocks act like the watches and clocks you have: they are able to keep 24 hours a day, and when you travel to different time zones, they are able to adjust to the local time

 

The microarray of expressed genes of young seedlings grown in constant light and temperature show their 10% of the genes circadian expression of steady state mRNA; the  peak expression varies just as clock regulated physiological pathways show peak activities at diverse time of the day.