11Biological ClocksLu Chen, Ph.D.MCB, UC Berkeley2What is biological clock?All eukaryotes and some prokaryotes display changes in gene activity, biochemistry, physiology, and behavior that wax and wane through the cycle of days and nights – circadian rhythm.Circadian rhythmicity is universally associated with the ability to perceive light, and the oscillators (“clocks”) giving rise to these rhythms, which are feedback loops based on transcription and translation, are reset by light.Examples: •the level of the hormone melatoninthat rises in your body during the night and falls during the day. •fruit flies (Drosophila) hatch in greatest numbers just at dawn.Even when the organism is placed in constant conditions (e.g., continuous darkness), these rhythms persist. However, without environmental cues, they tend to be somewhat longer or somewhat shorter than 24 hours - giving rise to the name circadian rhythms (L. circa = about; dies = day).23Circadian rhythms• The most important property is the ability to maintain self-sustained oscillations.• That is, under constant conditions, the rhythm continues with its natural frequency.• Can be reset by environmental cues, such as light.4What do circadian rhythms control?• Wake/sleep• Hormonal• Temperature• Immune• Drug metabolism• Renal function72-hour sleep deprivation060035Circadian rhythms -- free run6Circadian Rhythms- Various Species47In humans and other animals, the suprachiasmatic nucleus (SCN) controls most circadian rhythms such as rest-activity and drinking rhythm. -- If the SCN is isolated from the rest of the brain by means of knife cuts in vivo, circadian rhythms in single unit activity persist in the resultant "hypothalamic island," while rhythms in unit activity in other brain regions disappear.-- Lesions of the SCN eliminate circadian rhythmicity in rodents.-- Circadian rhythmicity is restored by transplantation of fetal SCN tissue. The newly restored rhythm is that of the donor.The SCN receives environmental light-dark information from the retino-hypothalamic tract. The cellular pathway by which light entrains the SCN pacemaker is unknown.Circadian rhythms – the pacemaker8Light Entrains the Human Biologic Clock(Retinohypothalamic tract)59Circadian rhythms after SCN lesion10• Melatonin is a hormone released from the pineal during darkness.• It is suppressed by exposure to light.• In some blinded individuals, it continues to be entrained to the external light/dark cycle.• Therefore, the retinohypothalamic tract may be intact, transmitting light/dark information to the SCN even though there is no conscious perception of vision.Melatonin and Circadian Rhythms611The Circadian Clock in DrosophilaA number of genes in Drosophila are turned on when the animal is exposed to light:•effector genes whose products mediate the animal's responses (e.g. hatching or molting) •clock genes whose products regulate the circadian clock. Three key members of this group are: •period (per) •timeless (tim) •vrille (vri)Activation of all of these genes requires that their promoters are bound by the protein transcription factors.•CLOCK encoded by the gene clock (clk) and •CYCLE encoded by the gene cycle (cyc)12The Circadian Clock in Drosophila – The MechanismThe CLK/CYC proteins are transcription factors for per, tim, vri and other effector genes.The PER and TIM proteins (synthesized on ribosomes in the cytoplasm) formdimers. •When the concentration of these gets high enough (early evening), they are transported into the nucleus. •The VRI protein also accumulates in the cytoplasm and goes into the nucleus, represses Clk gene transcription. In the nucleus, PER/TIM1) binds to the CLK/CYC transcription factors, removing them from the promoters of the genes they activate; thus shutting off transcription. Because these genes include per and tim, the result is a negative feedback loop; that is, the products of the per and tim genes inhibit their own synthesis. 2) Shuts off vri transcription, thus remove inhibition on clk gene transcription.3) As the level then falls, this inhibition is lifted and PER/TIM activity begins anew.71314•The time required for the different effects results in the levels of PER/TIM and CLOCK oscillating in opposite phases with a circadian (~24 hr) rhythm. The Circadian Clock in Drosophila – The Mechanism815The Circadian Clock in Drosophila – Setting The ClockEven without any external cues (e.g., alternating light and dark), the cycles persist although they tend to drift away from environmental time. •Under natural conditions, the clocks are precise. •This is because they are "set" (synchronized) by environmental cues, of which light is one of the most important.In Drosophila, it works like this. •Light (blue) is absorbed by the protein cryptochrome (CRY). •This causes an allosteric change in its conformation enabling it to bind to TIM. •This causes TIM to break down ending its inhibition on CYC/CLK. •If this happens when PER/TIM levels are rising (late in the "day"), it sets the clock back. •If it happens when PER/TIM levels are declining (late in the "night"). it sets the clock ahead. 16The Circadian Clock in MammalsThe circadian clock in mammals resembles that in Drosophila in a number of ways with many of the participating genes being homologous. However, there are some differences:The transcription factors that turn on the light-induced promoters are dimers of the CLOCK protein and a protein designated BMAL1. These dimers turn on- the per1 and per2 genes; - cry1 and cry2 genes, the gene encoding cryptochrome - rev-ERBα gene, whose product inhibits transcription of Bmal1- effector genes (such as the gene encoding vasopressin)The Per and Cry mRNAs are exported to the cytoplasm where they are translated. •The PER and CRY proteins then form dimers that enter the nucleus where they •turn OFF their own genes (as PER/TIM dimers do in Drosophila); •turn OFF Rev-erbαgene, thus removes the inhiibition on Bmal1transcription. So this double-negative effect causes the level of the BMAL1 protein to rise.•These actions cause the levels of BMAL1 and PER/CRY to oscillate in opposite phases (as CLOCK and PER/TIM do in Drosophila).917The Circadian Clock in Mammals18The Circadian Clock in Mammals - Setting The ClockIn mice, light acts through the retina and direct neural pathways to thesuprachiasmatic nuclei (SCN) to stimulate per gene expression.Mice who are