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WIKIPEDIA BIO154/254: Molecular and Cellular Neurobiology

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Pacemakers are internal biological oscillators in organisms that control the period and phase of some biological rhythms, such as the circadian rhythm and the heartbeat. These rhythms involve many separate oscillating systems (or cells in the case of the heartbeat) that are coordinated by the pacemaker. Thus pacemakers are ‘master clocks’. This controlling feature distinguishes pacemakers from the other types of biological oscillators.

The study of biological rhythms, which pacemakers control, is one of the oldest fields of science. They are mentioned in the writings of Aristotle (384-322 BC) (Ward, 1971). The periods of biological rhythms range from sub-microsecond in the electric organ of eels (Moortgat, 1998), to 24 hours in circadian rhythm, to 1 month in the menstrual cycle, to 12 months in hibernation, to longer than 1 year in the flowering cycle of bamboo (Fig. 1).
Figure 1. Image from (Engelmann, 2004).
Figure 1. Image from (Engelmann, 2004).
In the nervous system, rhythms underlie sensory coding, attention, memory and sleep (Fontanini, 2006). Rhythms are found in all organisms including bacteria (Engelmann, 2004), fungi, plants, insects, and mammals. Rhythms that are linked to external phenomena are called circa and those that are not are called non-circa (Hosn, 1997). Non-circa rhythms are not synchronized to external cycles but may still be influenced by external cues. Non-circa rhythms include the heartbeat.

It is likely that most or all of the biological rhythms in Fig. 1 are controlled by oscillators that have the defining characteristics of pacemakers listed above; however, it has not been common to refer to them all as pacemakers. The two most studied pacemakers are the circadian pacemaker and the cardiac pacemaker.

Circadian pacemaker

Circadian pacemakers coordinate the timing of biological events with the day/night cycle. Circadian rhythms are found in fungi, mammals, insects, fish, bacteria, and plants (Panda, 2002). Synchronizing an organism with the day/night cycle conveys selective advantages. For example, priming photosynthesis in plants before sunrise allows the maximum amount of light to be converted to useable energy (Merrow, 2005).

Defining Characteristics

Circadian pacemakers are self-sustaining, have a characteristic period, are capable of entrainment, and are temperature compensated.


Pacemakers will continue to oscillate in the absence of external cues. This is in contrast to external regulators of activity such as thermoregulation of lizard activity level by the warming of the sun.

Characteristic period

Circadian pacemakers have a period of approximately 24 hours. If kept in constant darkness, some mice will have a period of activity and rest that is slightly less than 24 hours (Pittendrigh, 1993).


Circadian pacemakers would not be useful if they were not synchronized with the day/night cycle. Therefore, despite being self-sustaining, circadian pacemakers can be entrained (synchronized) by input from external cues such as light or social activity. The mechanisms of light entrainment are the same for yeast and Drosophila but different for mammals.

Temperature compensation

Despite being based on biochemical reactions that are individually temperature sensitive, the circadian pacemaker is relatively insensitive to temperature variations.


The earliest record of an observation of a circadian pacemaker was made by de Mairan, a French astronomer, in 1729 (Hosn, 1997). He observed that clover leaves moved even in total darkness, despite the fact that the purpose of their movement seemed to be to track the sun. Linaeus (1707-1778) introduced the concept of a ‘flower clock’. In 1914 Szymanski showed that even under constant light conditions goldfish had a circadian rhythm. A genetic basis for circadian rhythms was indicated in experiments with bean plants by Bunning in 1932. Experiments by Pittendrigh around 1954 showed that the circadian rhythm in Drosophila was temperature compensated. Experiments by Ronald J. Konopka in Seymour Benzer’s lab identified a gene in which mutations caused an alteration of the circadian pacemaker’s period, and was thus named period (per). Different mutations of per either shortened or lengthened the period, or abolished the rhythm altogether (Chandrashekaran, 1999). Since then many other genes involved in circadian pacemaker have been identified in various species.


The locations of the circadian pacemakers in Drosophila and mice are shown in Fig. 3.
Figure 3. Image from (Panda, 2002).
Figure 3. Image from (Panda, 2002).

The circadian pacemaker in Drosophila is composed of six cell types, with only between 4 and 40 cells of each type (Fig. 2a). One of these types controls the morning activity level, three are synchronized with the evening activity level, and the other two have unknown function (Stoleru, 2005). In mice, the suprachiasmatic nuclus (SCN) of the hypothalamus contains the circadian pacemaker (Fig. 2b, c).


A unifying theme in circadian pacemaker mechanisms is a transcription/translation feedback loop found in fungi, insects, and mammals (Fig. 3).
Figure 3. Image from (Dunlap, 1998).
Figure 3. Image from (Dunlap, 1998).
The binding of PAS proteins to DNA causes transcription of clock proteins, which inhibit the PAS proteins and are degraded. This results in an oscillation, whose period is determined by how long it takes to degrade the clock proteins. The rate of clock protein degradation depends on their rate of phosphorylation. The details differ among species, and are as follows.

1) Drosophila

Since the pacemaker gene, per, was identified in Drosophila, it is one of the best understood mechanisms. The period of the clock is tuned by the multiple phosphorylation of per. Entrainment (phase) is modulated by the light-induced degradation of Timeless protein. The proposed mechanism is outlined in Fig. 4.
Figure 4. Image from (Bae, 2006).
Figure 4. Image from (Bae, 2006).

2) Mice

The SCN controls circadian oscillators in the retina, liver, heart, lung (Peirson, 2006), and kidney (Merrow, 2005). Circadian pacemakers control circulating hormone levels, cognitive and locomotor activity levels. Circadian pacemakers make use of a transcription/translation feedback loop. Several experiments in which single cells are isolated have shown that single cells can generate circadian rhythms of gene expression and circadian pacemakers are thus composed of a collection of single-cell circadian rhythm generators. The mechanism within each cell is diagrammed in Fig. 5.
Figure 5. Image from (Ko, 2006).
Figure 5. Image from (Ko, 2006).
The period of the clock is again tuned by the multiple phosphorylation of Per. The output is transcription rate of clock controlled genes (Ccgs).

3) Fungi

The network in yeast is shown in Fig. 6.
Figure 6. Image from (Dunlap, 2006).
Figure 6. Image from (Dunlap, 2006).

4) Fish

Many of the clock genes in mammals have homologs in zebrafish and the interactions are largely similar (Cahill, 2002).

Involvement of Circadian Pacemaker Genes in Other Biological Rhythms

There is evidence from Drosophila that the circadian rhythm genes may also affect the duration of biological events that occur on a much shorter time scale than the diurnal period. Kyriacou and Hall (1980) reported that mutations in the clock gene period affected the interval between pulses during male courtship "pulse song". Though this result was intially met with skepticism, the effect of period on interpulse interval has held up to scrutiny (see Kyriacou et al., 1990).

The genes period and timeless also have an effect on courtship duration. Males that are homozygous for null per or tim copulate significantly longer than wildtype males (Beaver and Giebultowicz, 2004). This effect seems to occur outside of the canonical clock mechanism. The courtship song and duration phenotypes of period mutants suggest that they might operate in a separate rhythm-generating pathway in addition to the clock cycle. In should be noted, however, that these genes are expressed during development and may have developmental effects on the neural substrates of these behaviors.

Cardiac pacemakers

There are two cardiac pacemakers, a primary and secondary; the secondary acts as a backup should the primary cease to function. The cardiac pacemaker uses a different mechanism than the circadian pacemaker, which accounts for their different periods. The cardiac pacemaker is similar to the circadian pacemaker in that it controls many other oscillators, the cells of the heart, each of which has the ability to generate spontaneous rhythmic depolarization. The cardiac pacemaker cells in the sinoatrial node control the heart rate because they have a faster rhythm than the other cells in the heart, thus forcing them to depolarize before they normally would. A secondary cardiac pacemaker is in the atrioventricular node and acts as a backup in case the primary pacemaker fails. The mechanism that causes spontaneous depolarization is based on the unique properties of the potassium, sodium, and calcium channels in the pacemaker cells of the heart. The cells spontaneously depolarize due to both a feedback mechanism in which the rate of potassium eflux decreases as the cell depolarizes, depolarizing it further, and a ‘funny current’, which results from sodium leaking in.

Artificial pacemakers

Artificial pacemakers are currently made using microelectronics; however, genetically engineered pacemakers may begin to replace microelectronic pacemakers (Boink, 2006).


Artificial pacemakers made with microelectronics are used in patients with irregular heartbeat, for example, when the sinus node of the heart does not function correctly.


Micoelectronic pacemakers implanted in the brain of epilepsy patients within 1 mm of the locations at which the seizures originate can help prevent seizures (


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