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BIOLOGICAL CLOCK - Is the Need for a Clock a Common Issue for Cells and Computers ?

BIOLOGICAL CLOCK - Is the Need for a Clock a Common Issue for Cells and Computers ? The recurrent 24 hours oscillations of biological activities which are generally called circadian rhythms are considered to be a mechanism allowing synchronisation of biological processes. The oscillations are generated by operation of special clock-like intra-cell devices comprising commonly transcription-translation processes as basis of measuring the time. The clock mechanism is controlled by two cooperating working out-of-phase negative feedback loops. Directly the oscillations are driven by steering signals changing the adjustment of feedback loops. They are created de novo in each cycle by complexation of synthesized proteins after their concentration reaches suitably high values. The complexes inhibit the protein synthesis in the own system while inducing it simultaneously in the cooperating one initiating in this way the next oscillation wave. The inhibition of protein synthesis is correlated with the degradation of already synthesizes molecules allowing the return to starting point of oscillation. The alignment of the proper phase of peripheral tissue cells clocks is maintained by the central brain clock ­ master clock. KEYWORDS: Circadian rhythms, biological clock, feedback inhibition control, steering signals. Introduction Developments in biological science enable us to better understand natural phenomena, contributing to technical and medical breakthroughs. One of the key problems currently being investigated in biology concerns the properties of biological clocks. Despite the intuitive nature of such mechanisms, neither their operation nor their biological role is sufficiently well understood. The presence of a biological clock manifests itself as a recurrent 24-hour oscillation of biological activity known as the circadian rhythms. While each cell has access to an independent clock oscillator, in higher-order organisms (such as animals) these oscillators are collectively and adaptively synchronized by a dedicated neural structure located in the suprachiasmatic nucleus of the hypothalamus. Metabolic processes and ­ in particular ­ protein synthesis are the primary means by which organisms are capable of measuring time. Synthesis of clock proteins is first up-regulated and then down-regulated in an alternating cycle. This oscillation is controlled by intrinsic signals, unlike in other than clock-like mechanisms associated with protein synthesis and degradation, which are subject to external control. These intrinsic signals (needed to switch the system off or on) are generated by way of protein complexation, once the accumulation of synthesized proteins reaches a critical threshold. According to the presented model, circadian rhythms are the outcome of two cooperating feedback loops, running out of phase with each other. Products of the clock gene downregulate their own expression while simultaneously activating the expression of a gene in a cooperating system. This mechanism drives periodic oscillations, which tend to behave in a similar way in most organisms, despite differing molecular representations. The role of the biological clock resembles that of a computer clock: its goal is to ensure synchronization of interlinked processes (such as energy supply and consumption, as well as transcription processes affecting metabolism). There is, however, another specific reason for cyclic metabolic changes: this is the need to keep cells in a permanent state of alertness, preventing excessive strengthening of metabolic connections which develop as an adaptation to persistent environmental conditions but makes the cell incapable of responding to sudden changes. The physiological capability of biological systems to adapt to circadian rhythms is readily evident in nature, although the existence of specialized clocklike mechanisms located in the brain (and in peripheral cells) has only recently turned the attention to the real significance of the problem. The fact that cyclic changes occur even in the most primitive organisms (such as bacteria) and in anucleate cells (e.g. erythrocytes) hints at the physiological importance of this mechanism and has been the focus of extensive research. Nevertheless, despite the scientific tools brought to bear on the problem, many of its aspects remain elusive. For instance it is not clear why cyclic modulation of biological processes is so crucial as to be ubiquitous in the living world and why evolution has generated special structures and mechanisms whose only purpose is to enforce such modulation [1]. The persistent, cyclic nature of changes suggests that the process is automatic. It should be noted that most biological systems rely on negative feedback loops (a well-known concept in the theory of automata). While however the entire machinery of life bases on some form of automatic control, the cycles generated by the biological clock possess some special, distinguishing characteristics associated with their intended role [1, 2]. All biological processes are subject to the laws of physics and chemistry. Being mostly reversible in nature (except for special cases), they naturally gravitate toward a state of equilibrium. Any chemical or physical reaction which reaches this state effectively ceases ­ which means that also processes occurring in a living cell can not attain equilibrium as their spontaneity (given by Gibbs' parameter, G) would become 0, implying the cessation of life. Biology therefore requires mechanisms which act to upset balance and enable cells to continue functioning, by replenishing substrates and eliminating the products of chemical reactions. This can be achieved in a thermodynamically open system (such as the living cell), however the process requires a means of automatic control by a negative feedback loop, ensuring a steady supply of components. Since the same logic applies to a great majority of biological processes, it should come as no surprise that negative feedback loops are the very foundation of life. A negative feedback loop can be said to exist if the process in question includes a receptor capable of down-regulating a given reaction as a response to the excess of its own product (Figure 1). In a complex system, such as the living cell, multiple negative feedback loops may affect one another. The result is a sophisticated network of mutual dependencies which, in order to function as a whole, requires synchronization based on a common measure of time. Providing such a measure is the primary purpose of biological clocks ­ comparable to the action of a CPU clock which synchronizes data processing and transfer in the computer system. Much like a computer, the cell must also be able to execute a large number of operations at precisely the right time. At the core of any clock lies some regular oscillator. This can be an hourglass, a pendulum, a piezo-electrical tool or another device which feeds an input signal to a synchronizing mechanism. In biological systems, the oscillator can be implemented by means of the accumulation and elimination of reaction products. In order to be useful as a time measurement device, the oscillator must conform to specific requirements. It has to produce repeatable, unambiguous oscillations with a clearly defined amplitude and frequency. While however the action of a biological oscillator bases on a negative feedback loop, "plain" loops are not sufficient as they simply counteract changes in the concentration of products which may not be regular and therefore cannot accurately measure circadian rhythms. Figure 1. The symbolic presentation of feedback inhibition loop at two different activity levels of stabilized process ­ the lower (gray) and its turned up form of higher activity (black) obtained as the result of alteration the receptor sensitivity by steering signal. Black box ­ effector system. Arrows represent oscillations of stabilized parameter around the programmed level. Discussion The regular variability of oscillations in biological clocks can however be acquired as a consequence of steering, thus the control over the desired set point of the parameter which is subject to stabilization by feedback inhibition (Figure 1). The steering signal may change the programmed level of parameter stabilized by feedback inhibition as for example concentration of the given product. A simple technical analogue is the action of a thermostat or refrigerator: which left alone automatically regulate temperature by implementing a negative feedback loop; however each can also receive steering signals, e.g. request to increase or decrease the set-point temperature, issued by a human operator or an external feedback loop. Referring to commonly known biological systems, the same phenomenon explains pyrexia (fever) which often accompanies infection. The subjective cold feeling is a result of the thermal regulatory receptor being "reprogrammed" to perceive core body temperature as too low, leading to a temperature increase. Once the infectious agent is eliminated from the organism, the temperature receptor subunit can be reset to its original value. In the case of fever, the steering signal is a specific bacterial toxin. Negative feedback loops stabilize body temperature regardless of the presence of toxins, but their set point is altered during infections. In both systems described above the steering signal is external to the feedback loop which performs regulation. However, in a true biological clock the signal is generated in a cyclic way, de novo inside the system. The cyclic nature of biological clocks is therefore a result of self-control by autosteering. The steering signals are created from synthesized proteins by their complexation after concentration crosses a critical threshold. Typically, these complexes are heterogeneous, which means that they consist of different proteins synthesized at the same time. The requirement of heterogeneity ensures higher specificity of the resulting signal. This is in agreement with the general principle which states that the signal becomes more specific and its lasting is shorter when the number of events required for its generation increases. The required coincidence of events (in this case ­ heterocomplexation) reduces signal duration and enables the mechanism to function as a "switch". An important factor in this scope is the rapid nature of the switching process (i.e. the steepness of the signal slope). This property depends convincingly on the complexation process of sigmoid kinetics (hence with the increasing steepness of slope). For example, the formation of key clock protein complex PER/CRY pentamers accelerates once the substrate proteins PER and CRY reach sufficiently high concentrations. This, in turn, leads to the synthesis process being abruptly halted by its own products. Similar kinetics are likely associated with proteins forming CLOCK/BMAL heterocomplex. Such kinetics is needed to produce distinct, repeatable oscillations (Figure 2). Another important mechanism which alters the properties of the proteins being synthesized and enables them to perform the role of signals is phosphorylation ­ capable of modifying the structure of resulting complexes and as well deciding of their degradation [1,3]. To-date scientific knowledge enable us to distinguish two cooperating regulatory mechanisms involved in the operation of biological clocks: the loop which regulates synthesis of transcription factors known in humans as BMAL and CLOCK, and the loop which regulates synthesis of primary clock proteins PER and CRY. Their complexes, both BMAL/CLOCL and PER/CRY perform the role of steering signals once their concentrations reach sufficiently high levels. The importance of PER and CRY proteins (as well as their analogues in other species) results from their involvement in intracellular processes and, specifically, from their role in biological clock system [4,5]. Figure 2. The mechanism of the biological clock shown in schematic representation as two step process ­ the first connected with the synthesis of protein components for the formation of CLOCK/BMAL complex and the second for PER/CRY complexation. The symbols and and inducing and stop signal. Following synthesis, the proteins form a heterocomplex consisting of three PER and two CRY molecules. The structure is very large, with an approximate mass of 1 megadalton. It acts to down-regulate synthesis of its own components and as well induces their degradation [6]. Simultaneously it initiates the next cycle by triggering the synthesis of CLOCK and BMAL proteins. The exact mechanism of action is unclear ­ it seems unlikely that a single protein complex would be able to perform all the listed functions in the cell. Perhaps it exists in various permutations (note that both PER and CRY are inhomogeneous and additionally may perhaps be modified, much like histones, through acetylation or methylation) [7,8]. Furthermore, the synthesis of PER and CRY varies over time, which may lead to creation of various complex subtypes, enabling many events to occur in a sequential fashion. Thus finally it appears that the cycle is initiated by synthesis of BMAL and CLOCK transcription factor components. Once the components reach sufficient concentrations, the BMAL/CLOCK complex emerges and triggers synthesis of PER and CRY proteins. At the same time, it down-regulates its own expression, likely by acting as an inhibitor. Degradation of CLOCK/BMAL and PER/CRY is reported to be initiated and induced by phosphorylation [3]. Figure 2 presents a model view depicting the action of biological clock. We assume that the clock mechanism is based on two out-of-phase negative feedback loops (as explained above) and that these loops operate in a standard manner, by regulating transcription and translation processes. According to the principle of negative feedback, their purpose is to stabilize the concentration of a specific product (in the clock system mostly RNA or protein). This is conventionally represented in Figure 3 by bars of equal height (lighter fragments). The target concentrations of proteins BMAL and CLOCK from the one site and PER and CRY from the other are reached in syntheses triggered mutually by PER/CRY and CLOCK/BMAL complexes as steering signals. The increased concentrations of proteins resulting from set point changes are represented by additional segments in Figure 3 (darker fragments), while the resulting concentration of proteins, enabling generation of signals by complexation, is marked in black at the top of bars. Figure 3. The out-of-phase oscillation of the clock proteins concentration presented in a conventional way by bars with fragments corresponding to basic unchanging concentration (lower - light gray) and concentration altered by steering signals (upper - dark gray). The black top part of bars corresponds to concentration allowing protein complexation and thus creation of steering signals. The symbols and represent the inducing and the stop signals. Above the corresponding oscillation represented as pendulum. The oscillating pendulum above. It appears that the principal role of the clock system is to synchronize intracellular processes [9-15]. However, there is another important reason why biological clocks are indispensable in nature ­ namely the need to maintain cells in a state of alertness. Intracellular processes, while very diverse, function as a coherent whole because their control loops are interdependent: the products of one process may directly control other processes by acting as allosteric effectors. The result is a complex network of dependencies which naturally gravitates towards a state of reinforced stability in accordance with its biological programming. However, there is a downside: the stronger the dependencies between individual processes the more inert the system becomes. This phenomenon can be compared to the reduction in anxiety with which societies approach potential disasters (earthquakes, floods etc.) following a long period of calm. The role of periodic disaster drills is to counteract this tendency ­ much like the circadian rhythms, which shape the activity of biological systems. Similar outcomes can be observed e.g. in the long-term readjustment of metabolic activity which accompanies hibernation in certain mammals, as well as the altered metabolic pathways associated e.g. with production of plant seeds, pupation of insects or even formation of germ cysts [16-18]. Hibernation is an effect which may take a surprisingly long amount of time to recover from: for instance, the brown bear requires approximately 3 weeks during spring to resume normal activity [19]. This suggests that metabolism ­ both cellular and systemic ­ is a highly complex system which aligns itself to environmental conditions and, once fully aligned, does not easily admit changes. While long-term adaptation increases the efficiency of operation under a given set of conditions, it does so at the cost of reduced capacity for change. Circadian rhythms act as an efficient regulatory mechanism, counteracting this tendency. The cyclic nature of metabolism and other processes is not specifically tied to transcription. Indeed, there is ample evidence for cyclic posttranslation mechanisms based on the action of enzymes, which reinforces the biological importance of circadian rhythms. For instance, a post-translation circadian cycle has been described in cyanobacteria, where it affects oligomerization and phosphorylation of proteins [20]. The role of biological oscillators is further highlighted by the properties of red blood cells, whose metabolism (for obvious reasons) differs from that of nucleated cells, but which nevertheless undergo cyclic changes. As can be expected, in erythrocytes this property hinges upon oxidation and reduction, mediated by peroxiredoxins ­ special enzymes which protect the cell from oxygen radicals. Hemoglobin itself is capable of periodically altering its susceptibility to oxidation likely by dissociating into dimeric subunits [21,22]. In addition to circadian oscillations there are also various accessory subsystems, capable of resetting biological clocks or adjusting their accuracy to more closely follow natural daylight changes [23-28]. The role of clocks in cell division and in processes which involve significant reduction of metabolic activity (such as hibernation) remains a poorly understood topic despite its self-evident importance. In most animals tissue-specific peripheral clocks are all synchronized by the so-called "master" clock, located in the suprachiasmatic nucleus of the brain. It operates on the same principles as other biological clocks, though it is also capable of adjusting itself to daylight cycles by registering the intensity of ambient light [29]. Some surveying devices which rely on protein synthesis and degradation but which do not track daylight changes are also known in biology. One example is the action of cyclins which assist cell division [30]. This mechanism, while somewhat similar to the action of biological clocks, does not measure time ­ rather, it registers the progression and completion of individual stages of cell division. A clock-like mechanism is also "built into" hormonal signals: thus G protein components bind to adenylate cyclase and kinases, triggering GTP-ase activity which inactivates the hormonal action after a predetermined amount of time (acting as a "cutoff valve" [31]). Another system which appears to acknowledge the passage of time is the telomere, despite the lack of similarity to original clocks [32]. Also, oscillations other than circadian are often observed to be used in synchronization of developmental processes indicating to oscillations as the important biological mechanism [33-37]. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bio-Algorithms and Med-Systems de Gruyter

BIOLOGICAL CLOCK - Is the Need for a Clock a Common Issue for Cells and Computers ?

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Abstract

The recurrent 24 hours oscillations of biological activities which are generally called circadian rhythms are considered to be a mechanism allowing synchronisation of biological processes. The oscillations are generated by operation of special clock-like intra-cell devices comprising commonly transcription-translation processes as basis of measuring the time. The clock mechanism is controlled by two cooperating working out-of-phase negative feedback loops. Directly the oscillations are driven by steering signals changing the adjustment of feedback loops. They are created de novo in each cycle by complexation of synthesized proteins after their concentration reaches suitably high values. The complexes inhibit the protein synthesis in the own system while inducing it simultaneously in the cooperating one initiating in this way the next oscillation wave. The inhibition of protein synthesis is correlated with the degradation of already synthesizes molecules allowing the return to starting point of oscillation. The alignment of the proper phase of peripheral tissue cells clocks is maintained by the central brain clock ­ master clock. KEYWORDS: Circadian rhythms, biological clock, feedback inhibition control, steering signals. Introduction Developments in biological science enable us to better understand natural phenomena, contributing to technical and medical breakthroughs. One of the key problems currently being investigated in biology concerns the properties of biological clocks. Despite the intuitive nature of such mechanisms, neither their operation nor their biological role is sufficiently well understood. The presence of a biological clock manifests itself as a recurrent 24-hour oscillation of biological activity known as the circadian rhythms. While each cell has access to an independent clock oscillator, in higher-order organisms (such as animals) these oscillators are collectively and adaptively synchronized by a dedicated neural structure located in the suprachiasmatic nucleus of the hypothalamus. Metabolic processes and ­ in particular ­ protein synthesis are the primary means by which organisms are capable of measuring time. Synthesis of clock proteins is first up-regulated and then down-regulated in an alternating cycle. This oscillation is controlled by intrinsic signals, unlike in other than clock-like mechanisms associated with protein synthesis and degradation, which are subject to external control. These intrinsic signals (needed to switch the system off or on) are generated by way of protein complexation, once the accumulation of synthesized proteins reaches a critical threshold. According to the presented model, circadian rhythms are the outcome of two cooperating feedback loops, running out of phase with each other. Products of the clock gene downregulate their own expression while simultaneously activating the expression of a gene in a cooperating system. This mechanism drives periodic oscillations, which tend to behave in a similar way in most organisms, despite differing molecular representations. The role of the biological clock resembles that of a computer clock: its goal is to ensure synchronization of interlinked processes (such as energy supply and consumption, as well as transcription processes affecting metabolism). There is, however, another specific reason for cyclic metabolic changes: this is the need to keep cells in a permanent state of alertness, preventing excessive strengthening of metabolic connections which develop as an adaptation to persistent environmental conditions but makes the cell incapable of responding to sudden changes. The physiological capability of biological systems to adapt to circadian rhythms is readily evident in nature, although the existence of specialized clocklike mechanisms located in the brain (and in peripheral cells) has only recently turned the attention to the real significance of the problem. The fact that cyclic changes occur even in the most primitive organisms (such as bacteria) and in anucleate cells (e.g. erythrocytes) hints at the physiological importance of this mechanism and has been the focus of extensive research. Nevertheless, despite the scientific tools brought to bear on the problem, many of its aspects remain elusive. For instance it is not clear why cyclic modulation of biological processes is so crucial as to be ubiquitous in the living world and why evolution has generated special structures and mechanisms whose only purpose is to enforce such modulation [1]. The persistent, cyclic nature of changes suggests that the process is automatic. It should be noted that most biological systems rely on negative feedback loops (a well-known concept in the theory of automata). While however the entire machinery of life bases on some form of automatic control, the cycles generated by the biological clock possess some special, distinguishing characteristics associated with their intended role [1, 2]. All biological processes are subject to the laws of physics and chemistry. Being mostly reversible in nature (except for special cases), they naturally gravitate toward a state of equilibrium. Any chemical or physical reaction which reaches this state effectively ceases ­ which means that also processes occurring in a living cell can not attain equilibrium as their spontaneity (given by Gibbs' parameter, G) would become 0, implying the cessation of life. Biology therefore requires mechanisms which act to upset balance and enable cells to continue functioning, by replenishing substrates and eliminating the products of chemical reactions. This can be achieved in a thermodynamically open system (such as the living cell), however the process requires a means of automatic control by a negative feedback loop, ensuring a steady supply of components. Since the same logic applies to a great majority of biological processes, it should come as no surprise that negative feedback loops are the very foundation of life. A negative feedback loop can be said to exist if the process in question includes a receptor capable of down-regulating a given reaction as a response to the excess of its own product (Figure 1). In a complex system, such as the living cell, multiple negative feedback loops may affect one another. The result is a sophisticated network of mutual dependencies which, in order to function as a whole, requires synchronization based on a common measure of time. Providing such a measure is the primary purpose of biological clocks ­ comparable to the action of a CPU clock which synchronizes data processing and transfer in the computer system. Much like a computer, the cell must also be able to execute a large number of operations at precisely the right time. At the core of any clock lies some regular oscillator. This can be an hourglass, a pendulum, a piezo-electrical tool or another device which feeds an input signal to a synchronizing mechanism. In biological systems, the oscillator can be implemented by means of the accumulation and elimination of reaction products. In order to be useful as a time measurement device, the oscillator must conform to specific requirements. It has to produce repeatable, unambiguous oscillations with a clearly defined amplitude and frequency. While however the action of a biological oscillator bases on a negative feedback loop, "plain" loops are not sufficient as they simply counteract changes in the concentration of products which may not be regular and therefore cannot accurately measure circadian rhythms. Figure 1. The symbolic presentation of feedback inhibition loop at two different activity levels of stabilized process ­ the lower (gray) and its turned up form of higher activity (black) obtained as the result of alteration the receptor sensitivity by steering signal. Black box ­ effector system. Arrows represent oscillations of stabilized parameter around the programmed level. Discussion The regular variability of oscillations in biological clocks can however be acquired as a consequence of steering, thus the control over the desired set point of the parameter which is subject to stabilization by feedback inhibition (Figure 1). The steering signal may change the programmed level of parameter stabilized by feedback inhibition as for example concentration of the given product. A simple technical analogue is the action of a thermostat or refrigerator: which left alone automatically regulate temperature by implementing a negative feedback loop; however each can also receive steering signals, e.g. request to increase or decrease the set-point temperature, issued by a human operator or an external feedback loop. Referring to commonly known biological systems, the same phenomenon explains pyrexia (fever) which often accompanies infection. The subjective cold feeling is a result of the thermal regulatory receptor being "reprogrammed" to perceive core body temperature as too low, leading to a temperature increase. Once the infectious agent is eliminated from the organism, the temperature receptor subunit can be reset to its original value. In the case of fever, the steering signal is a specific bacterial toxin. Negative feedback loops stabilize body temperature regardless of the presence of toxins, but their set point is altered during infections. In both systems described above the steering signal is external to the feedback loop which performs regulation. However, in a true biological clock the signal is generated in a cyclic way, de novo inside the system. The cyclic nature of biological clocks is therefore a result of self-control by autosteering. The steering signals are created from synthesized proteins by their complexation after concentration crosses a critical threshold. Typically, these complexes are heterogeneous, which means that they consist of different proteins synthesized at the same time. The requirement of heterogeneity ensures higher specificity of the resulting signal. This is in agreement with the general principle which states that the signal becomes more specific and its lasting is shorter when the number of events required for its generation increases. The required coincidence of events (in this case ­ heterocomplexation) reduces signal duration and enables the mechanism to function as a "switch". An important factor in this scope is the rapid nature of the switching process (i.e. the steepness of the signal slope). This property depends convincingly on the complexation process of sigmoid kinetics (hence with the increasing steepness of slope). For example, the formation of key clock protein complex PER/CRY pentamers accelerates once the substrate proteins PER and CRY reach sufficiently high concentrations. This, in turn, leads to the synthesis process being abruptly halted by its own products. Similar kinetics are likely associated with proteins forming CLOCK/BMAL heterocomplex. Such kinetics is needed to produce distinct, repeatable oscillations (Figure 2). Another important mechanism which alters the properties of the proteins being synthesized and enables them to perform the role of signals is phosphorylation ­ capable of modifying the structure of resulting complexes and as well deciding of their degradation [1,3]. To-date scientific knowledge enable us to distinguish two cooperating regulatory mechanisms involved in the operation of biological clocks: the loop which regulates synthesis of transcription factors known in humans as BMAL and CLOCK, and the loop which regulates synthesis of primary clock proteins PER and CRY. Their complexes, both BMAL/CLOCL and PER/CRY perform the role of steering signals once their concentrations reach sufficiently high levels. The importance of PER and CRY proteins (as well as their analogues in other species) results from their involvement in intracellular processes and, specifically, from their role in biological clock system [4,5]. Figure 2. The mechanism of the biological clock shown in schematic representation as two step process ­ the first connected with the synthesis of protein components for the formation of CLOCK/BMAL complex and the second for PER/CRY complexation. The symbols and and inducing and stop signal. Following synthesis, the proteins form a heterocomplex consisting of three PER and two CRY molecules. The structure is very large, with an approximate mass of 1 megadalton. It acts to down-regulate synthesis of its own components and as well induces their degradation [6]. Simultaneously it initiates the next cycle by triggering the synthesis of CLOCK and BMAL proteins. The exact mechanism of action is unclear ­ it seems unlikely that a single protein complex would be able to perform all the listed functions in the cell. Perhaps it exists in various permutations (note that both PER and CRY are inhomogeneous and additionally may perhaps be modified, much like histones, through acetylation or methylation) [7,8]. Furthermore, the synthesis of PER and CRY varies over time, which may lead to creation of various complex subtypes, enabling many events to occur in a sequential fashion. Thus finally it appears that the cycle is initiated by synthesis of BMAL and CLOCK transcription factor components. Once the components reach sufficient concentrations, the BMAL/CLOCK complex emerges and triggers synthesis of PER and CRY proteins. At the same time, it down-regulates its own expression, likely by acting as an inhibitor. Degradation of CLOCK/BMAL and PER/CRY is reported to be initiated and induced by phosphorylation [3]. Figure 2 presents a model view depicting the action of biological clock. We assume that the clock mechanism is based on two out-of-phase negative feedback loops (as explained above) and that these loops operate in a standard manner, by regulating transcription and translation processes. According to the principle of negative feedback, their purpose is to stabilize the concentration of a specific product (in the clock system mostly RNA or protein). This is conventionally represented in Figure 3 by bars of equal height (lighter fragments). The target concentrations of proteins BMAL and CLOCK from the one site and PER and CRY from the other are reached in syntheses triggered mutually by PER/CRY and CLOCK/BMAL complexes as steering signals. The increased concentrations of proteins resulting from set point changes are represented by additional segments in Figure 3 (darker fragments), while the resulting concentration of proteins, enabling generation of signals by complexation, is marked in black at the top of bars. Figure 3. The out-of-phase oscillation of the clock proteins concentration presented in a conventional way by bars with fragments corresponding to basic unchanging concentration (lower - light gray) and concentration altered by steering signals (upper - dark gray). The black top part of bars corresponds to concentration allowing protein complexation and thus creation of steering signals. The symbols and represent the inducing and the stop signals. Above the corresponding oscillation represented as pendulum. The oscillating pendulum above. It appears that the principal role of the clock system is to synchronize intracellular processes [9-15]. However, there is another important reason why biological clocks are indispensable in nature ­ namely the need to maintain cells in a state of alertness. Intracellular processes, while very diverse, function as a coherent whole because their control loops are interdependent: the products of one process may directly control other processes by acting as allosteric effectors. The result is a complex network of dependencies which naturally gravitates towards a state of reinforced stability in accordance with its biological programming. However, there is a downside: the stronger the dependencies between individual processes the more inert the system becomes. This phenomenon can be compared to the reduction in anxiety with which societies approach potential disasters (earthquakes, floods etc.) following a long period of calm. The role of periodic disaster drills is to counteract this tendency ­ much like the circadian rhythms, which shape the activity of biological systems. Similar outcomes can be observed e.g. in the long-term readjustment of metabolic activity which accompanies hibernation in certain mammals, as well as the altered metabolic pathways associated e.g. with production of plant seeds, pupation of insects or even formation of germ cysts [16-18]. Hibernation is an effect which may take a surprisingly long amount of time to recover from: for instance, the brown bear requires approximately 3 weeks during spring to resume normal activity [19]. This suggests that metabolism ­ both cellular and systemic ­ is a highly complex system which aligns itself to environmental conditions and, once fully aligned, does not easily admit changes. While long-term adaptation increases the efficiency of operation under a given set of conditions, it does so at the cost of reduced capacity for change. Circadian rhythms act as an efficient regulatory mechanism, counteracting this tendency. The cyclic nature of metabolism and other processes is not specifically tied to transcription. Indeed, there is ample evidence for cyclic posttranslation mechanisms based on the action of enzymes, which reinforces the biological importance of circadian rhythms. For instance, a post-translation circadian cycle has been described in cyanobacteria, where it affects oligomerization and phosphorylation of proteins [20]. The role of biological oscillators is further highlighted by the properties of red blood cells, whose metabolism (for obvious reasons) differs from that of nucleated cells, but which nevertheless undergo cyclic changes. As can be expected, in erythrocytes this property hinges upon oxidation and reduction, mediated by peroxiredoxins ­ special enzymes which protect the cell from oxygen radicals. Hemoglobin itself is capable of periodically altering its susceptibility to oxidation likely by dissociating into dimeric subunits [21,22]. In addition to circadian oscillations there are also various accessory subsystems, capable of resetting biological clocks or adjusting their accuracy to more closely follow natural daylight changes [23-28]. The role of clocks in cell division and in processes which involve significant reduction of metabolic activity (such as hibernation) remains a poorly understood topic despite its self-evident importance. In most animals tissue-specific peripheral clocks are all synchronized by the so-called "master" clock, located in the suprachiasmatic nucleus of the brain. It operates on the same principles as other biological clocks, though it is also capable of adjusting itself to daylight cycles by registering the intensity of ambient light [29]. Some surveying devices which rely on protein synthesis and degradation but which do not track daylight changes are also known in biology. One example is the action of cyclins which assist cell division [30]. This mechanism, while somewhat similar to the action of biological clocks, does not measure time ­ rather, it registers the progression and completion of individual stages of cell division. A clock-like mechanism is also "built into" hormonal signals: thus G protein components bind to adenylate cyclase and kinases, triggering GTP-ase activity which inactivates the hormonal action after a predetermined amount of time (acting as a "cutoff valve" [31]). Another system which appears to acknowledge the passage of time is the telomere, despite the lack of similarity to original clocks [32]. Also, oscillations other than circadian are often observed to be used in synchronization of developmental processes indicating to oscillations as the important biological mechanism [33-37].

Journal

Bio-Algorithms and Med-Systems – de Gruyter

Published: Jan 1, 2012

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