The basic model of a biological clock consists of 3 parts – a central
oscillator that generates the rhythm, inputs that detect Zeitgebers and
entrain the oscillator, and outputs that translate the rhythm from the
oscillator into overt rhythms.
Although this basic model is rather an oversimplification, as inputs can
be outputs as well (e.g. photoreceptors), and outputs can feedback on the
oscillator, altering its pace, it is a good starting point for examining the
molecular clockwork of the clock.
The oscillator generates the rhythm of the biological clock. There are
two levels of regulation – negative feedback and post-transcriptional
control.
Negative feedback is when the protein product of a gene acts the gene itself
to down regulate its expression. This creates an oscillating pattern of gene
expression. Negative feedback occurs at least once in every biological
clock.
In some cases, the inhibition is direct, with the protein product of a
gene inhibiting its transcription. In other cases, the inhibition is
indirect. The protein product of a gene does not directly inhibit the gene.
Instead it inhibits another protein that is responsible for triggering the
transcription of its gene.
A generalised negative feedback loop.
The inhibition of the gene is either direct (a), with the protein directly
inhibiting its own transcription, or indirect (b) with the gene product
inhibiting a positive element that causes the transcription of the gene.
In both cases, the inhibition causes rhythmic transcription of the gene,
and rhythmic levels of the protein. The gene will be transcribed, causing an
increase in the amount of mRNA and protein up to a certain level. At this
point the protein inhibits the transcription of the gene. This reduces the
amount of mRNA and protein being produced. When the levels of protein are
reduced sufficiently, the inhibition of the gene is lifted and transcription
starts again.
The following chapters illustrate feedback loops in four different
organisms:
Cyanobacteria
Neurospora
Drosophila
Mammals
Although the feedback loops in themselves are enough to generate a
rhythmic signal, they cannot account for how a clock spans 24 hours.
Post-transcriptional control of the genes allows the clock to cycle with a
24 hour period, maintain the cycling of the clock components from
transcription to output and provides a buffer to abrupt changes that might
disrupt the clock.
Post transcriptional control also provides a way for the clock to be
reset by Zeitgebers.
There are 4 post-transcriptional mechanisms at work in the biological
clock:
Control of RNA - In some clocks cycling
occurs at the mRNA levels rather than the transcription level. This has been
shown particularly in Drosophila. There may also be alternate
splicing of mRNA according to environmental conditions such as cold or
light.
Translational control - In every
clock there is a delay between the peak levels of the mRNA of one gene and
the corresponding protein to allow levels of mRNA to accumulate before the
gene is repressed by negative feedback.
Nuclear translocation - In every known clock, a key step is the
translocation of a protein from the cytoplasm into the nucleus. In every
case the protein is part of the negative arm of the clock.
Protein degradation - Although the
cycling of many clock proteins is due to rhythmic expression, hand in hand
with this is the rapid degradation of proteins. All cycling proteins in any
biological clock have a short half-life, to prevent them from accumulating
until equilibrium is reached. In most cases the degradation is by the
ubiquitin-proteosome pathway, and the proteins are targeted for destruction
by progressive phosphorylation.
One of the key properties of a circadian rhythm is its ability to be
reset by external environmental cues (Zeitgebers). To do this the
environmental cues must be detected by detectors that must then translate
them into alterations in the activity of genes or proteins in the central
oscillator, either directly or via intermediate.
Although there are many different Zeitgebers (see
the “clock” section), the predominant one is nearly always light.
Light alters the phase of the oscillator by acting on the negative elements
of the feedback loop. This affects the phase of these elements and thus in
turn affects the phase of the oscillator. This is achieved either by light
degrading a clock component whose levels decline during the day (overcoming
the clock mechanisms that stabilises that protein), or indices a component
with levels that increase during the night (overcoming clock mediated
repression. In all clocks, the clock itself controls one or more of the
constituents of the resetting pathway. This means that a clock is more
susceptible to resetting at certain times of the day than others (e.g. dusk
and dawn). This property is known as gating of the light input.
The following chapter illustrate the light input pathways in four
different organisms:
Cyanobacteria
Neurospora
Drosophila
Mammals
Most outputs are generated using
the cis- and trans- acting elements to create cyclic transcription of output
genes. The products of these in turn act on other genes and systems to form
rhythmic cellular and physiological processes.
Although the systems regulated by
the biological clock vary from species to species, there are some systems
common to all of organisms. For example systems that help prevent genomic
damage by UV light from the sun, or genes that produce enzymes or hormones
that help regulate energy metabolism (Harmer et al. 2001), or mediate
coordination of carbon, nitrogen and sulphur pathways (Harmer et al 2000).
Many of these clock regulated genes also feedback on the oscillator, helping
to synchronise the clocks in different cells.
The following chapter illustrates
some of the output pathways in 4 different organisms:
Cyanobacteria
Neurospora
Drosophila
Mammals
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