Evolution of Biological Timing System

Evolution of biological timing system
• Circadian clocks enhance the innate ability of organisms to survive under ever-changing
environments by enabling them to efficiently anticipate periodic events such as availability of
food, light and mates.
• The mechanism of resetting of the clocks with varying time zones and cues occur in organisms
from bacteria to humans.
• Precisely timed rhythmic activities confer greater adaptive advantage compared to randomly
occurring activities, and in turn those clocks that enable organisms to maintain such phases are
selected.
• The last universal common ancestor and all the subsequent life forms that evolved from it,
including humans, have eternally experienced the diurnal changes in the form of day and
night
• Evolutionary pressures and natural selection have favored the formation of genetic circuits
that keep track of time and alter the physiology and behavior of life forms
• The genetic circuits that regulate the internal clock or pacemaker are conserved from
bacteria to plants and humans, though the individual components may differ
Adaptive functional significance of biological clocks
• Circadian clocks have evolved due to fitness advantage accrued in two ways
(i) by synchronizing its behavioral and physiological processes to cyclic
environmental factors to keep track of local time (extrinsic adaptive value)
(ii) by coordinating its internal metabolic processes (intrinsic adaptive value).
Examples:
• Experiments in cyanobacteria, show that in competition experiments,
strains that exhibit an internal clock periodicity, which is similar to external
environmental periodicity, have a better Darwinian fitness.
• Drosophila lines with a mutation in genes involved in the maintenance of

internal periodicity exhibit different rates of development as well as
differences in their lifespan.
• Continued long-term disturbances in a sleep–wake cycle of higher

animals have been linked to several disorders ranging from reduced
cognitive ability to a higher incidence of cancers.
• The daily Light/Dark cycles are believed to be the primary force behind the emergence and
maintenance of circadian clocks
• Since a number of cellular functions are affected by light, it was speculated that organisms
might have restricted some of their metabolic processes to night to avoid adverse effects
of light
• Several organisms are also known to shift various UV-sensitive cellular processes such as
DNA replication to night to avoid exposure to deleterious UV radiations. For example, the
unicellular alga Chlamydomonas reinhardtii
• Increased level of free oxygen in the early eukaryote evolution is believed to have
forced the organisms to minimize the deleterious effects of the diurnal photo oxidative
exposures by developing circadian rhythmicity of metabolic activities.
• Circadian clocks emerged in association with photoperiodic time measurement

mechanisms. The fact that several multicellular and a few unicellular organisms such
as photosynthetic unicellular Chlamydomonas exhibit photoperiodism renders
support to this hypothesis
• The temporal coordination of internal metabolic events is often cited as an important
benefit accrued from the circadian clocks
• Incompatible processes, which may require different physiochemical conditions for

their successful functioning, appear to be separated efficiently in time and space
with the aid of circadian clocks
• Molecular and genetic studies indicate that the 24h period arises from negative and
positive feedback loops controlling the transcription of clock genes.
Circadian rhythm in Cyanobacteria
• Circadian clocks are important for photosynthetic organisms like cyanobacteria (Blue-green
algae) and purple bacteria, the vital processes of which are dependent on photochemical
reactions
• Several species of Cyanobacteria are capable of photosynthesis and nitrogen fixation.

However, the enzymes involved in nitrogen fixation are inhibited in the presence of oxygen.
Hence, they resort to temporal separation of these two processes.
• Photosynthesis takes place during the daylight, while nitrogen fixation peaks during
night/dark.
• Cyanobacteria were the first prokaryotes reported to possess circadian
clocks controlled by a cluster of three genes, KaiA, KaiB, and KaiC
• KaiA, KaiB and KaiC along with two accessory proteins, help the algae
prepare for sunrise by stockpiling proteins needed for photosynthesis,
global patterns of gene expression and the timing of cell division
• Blue-green algae have one of the simplest circadian clocks, with three
protein gears. KaiA helps KaiC add phosphate (purple) to itself by
dusk. At night, KaiB blocks KaiA and the phosphates are stripped from
KaiC by dawn. This clock helps algae synchronize photosynthesis with
sunlight.
Circadian rhythm in Drosophila
• Drosophila melanogaster is a holometabolous insect having defined stages of

development from egg, to larva, then pupa, and finally to an adult.
• Inside the pupa, metamorphosis transforms it into a fly, which on development,

emerges from the pupa in a process called eclosion.
• It was observed that eclosion is ‘gated’ by the circadian clock, such that most flies
eclose 1–2 h before dawn.
• Further, the locomotor behavior assays show that wild-type flies are active during
the day/light and inactive during the night/dark in an LD (light–dark) cycle.
Behaviors regulated by circadian rhythms in Drosophila include:
• Locomotion
• Eclosion
• Mating
• Feeding and temperature preference
• Period (per) and timeless (tim) core genes are responsible for the circadian rhythm
• But TIM protein is light sensitive and accumulates only after dark and stabilizes
when it forms a dimer along with PERIOD. Again here, PER alone is unstable and
dimerization with TIM stabilizes it.
circadianly-regulated genes (CRGs)

• The rise of per and tim mRNA in the evening/dark phase leads to accumulation of PER
and TIM in the cytoplasm.
• Later, the TIM and PER heterodimers enter the nucleus and binds to Clk/Cyc dimers
via a Per-Clk interaction. This interaction causes hyperphosphorylation of the clock and
thus prevents Clk/Cyc dimers from binding to the DNA. This negatively regulates
transcription of per and tim genes.
• This creates a negative feedback loop where Period inhibits its own transcription.
• In the morning, light causes TIM degradation and without TIM, PER is less stable and
both are degraded by a proteasome dependent pathway
• PER and TIM degradation during light releases CLK/CYC from repression to start a new
cycle.
• This molecular clock receives one of the strongest environmental inputs, light, through the
activation of CRYPTOCHROME (CRY)
• Upon photon absorption, this blue-light photoreceptor undergoes a conformational
change that allows it to bind TIM.
• This promotes TIM ubiquitination and proteasomal degradation, thereby resetting the
clock
• The Nobel prize 2017 for physiology or medicine has been awarded to three neurogeneticists Jeffrey C.
Hall, Michael Rosbash and Michael W. Young who uncovered the mechanisms of the circadian clock in
Drosophila melanogaster.
• Importantly, the feedback loop mechanism is conserved in virtually all animal species and the mammalian
orthologs of the period, clock, cycle and double-time genes play a similar function.
• In mouse and human the forward loop consists of CLOCK (homolog of
dCLK) and BMAL1 (homolog of dCYC), which also form a heterodimeric
transcriptional activator.
• PERIOD and CRYPTOCHROME (CRY) homologs of which there are 3 and 2
respectively.
• Drosophila also uses a CRY that regulates transcription but also acts as a
photosensor. In mammals, light resets the clock by inducing a CREB-
dependent increase of per genes' transcription
Circadian rhythm in Birds
• Biological clock function in birds is critical for sleep/wake cycles, but may also regulate the acquisition of
place memory, learning of song from tutors, social integration, and time-compensated navigation.
• The avian circadian system is even more complex than that of mammals, involving pacemakers that
regulate peripheral tissues that are present in the pineal gland, the retina, and the SCN (which in birds
consists of two structures, the visual [v]SCN and medial [m]SCN.
• At the molecular level, avian biological clocks comprise a genetic network of “positive
elements” clock and bmal1 whose interactions with the “negative elements” period 2 (per2), period 3
(per3), and the cryptochromes form an oscillatory feedback loop that circumnavigates the 24 h of the day.
Birds
• In mammals, the SCN alone serves as a
pacemaker that receives light signals from the
retina through the RHT (whereas the light-
perceptive pineal gland and retina, together
with the SCN, form the pacemaker system in
birds), and directly regulates pineal melatonin
biosynthesis as an output of the clock.
Mammals
• In both mammals and birds, pineal melatonin

secretion is restricted to the night and, through
melatonin receptors expressed in the SCN,
inhibits night-time SCN activity
Circadian oscillators are controlled through a common mechanism

Evolution of Biological Timing System

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Evolution of biological timing system

• Drosophila lines with a mutation in genes involved in the maintenance of

• Continued long-term disturbances in a sleep–wake cycle of higher

• Circadian clocks emerged in association with photoperiodic time measurement

• Incompatible processes, which may require different physiochemical conditions for

• Several species of Cyanobacteria are capable of photosynthesis and nitrogen fixation.

• Drosophila melanogaster is a holometabolous insect having defined stages of

• Inside the pupa, metamorphosis transforms it into a fly, which on development,

circadianly-regulated genes (CRGs)

• In both mammals and birds, pineal melatonin

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