A circadian clock, or circadian oscillator, is a biochemical oscillator that cycles with a stable
phase
Phase or phases may refer to:
Science
*State of matter, or phase, one of the distinct forms in which matter can exist
*Phase (matter), a region of space throughout which all physical properties are essentially uniform
* Phase space, a mathematic ...
and is synchronized with
solar time
Solar time is a calculation of the passage of time based on the position of the Sun in the sky. The fundamental unit of solar time is the day, based on the synodic rotation period. Two types of solar time are apparent solar time (sundial ti ...
.
Such a clock's ''in vivo'' period is necessarily almost exactly 24 hours (the earth's current
solar day
A synodic day (or synodic rotation period or solar day) is the period for a celestial object to rotate once in relation to the star it is orbiting, and is the basis of solar time.
The synodic day is distinguished from the sidereal day, which is ...
). In most living things, internally synchronized circadian clocks make it possible for the organism to anticipate daily environmental changes corresponding with the day–night cycle and adjust its biology and behavior accordingly.
The term circadian derives from the Latin ''circa'' (about) ''dies'' (a day), since when taken away from external cues (such as environmental light), they do not run to exactly 24 hours. Clocks in humans in a lab in constant low light, for example, will average about 24.2 hours per day, rather than 24 hours exactly.
The normal body clock oscillates with an endogenous period of exactly 24 hours, it
entrains, when it receives sufficient daily corrective signals from the environment, primarily daylight and darkness. Circadian clocks are the central mechanisms that drive
circadian rhythm
A circadian rhythm (), or circadian cycle, is a natural, internal process that regulates the sleep–wake cycle and repeats roughly every 24 hours. It can refer to any process that originates within an organism (i.e., Endogeny (biology), endogeno ...
s. They consist of three major components:
* a central biochemical oscillator with a period of about 24 hours that keeps time;
* a series of input pathways to this central oscillator to allow
entrainment
Entrainment may refer to:
* Air entrainment, the intentional creation of tiny air bubbles in concrete
* Brainwave entrainment, the practice of entraining one's brainwaves to a desired frequency
* Entrainment (biomusicology), the synchronization o ...
of the clock;
* a series of output pathways tied to distinct phases of the oscillator that regulate overt rhythms in biochemistry, physiology, and behavior throughout an organism.
The clock is reset as an organism senses environmental time cues of which the primary one is light. Circadian oscillators are ubiquitous in tissues of the body where they are synchronized by both
endogenous
Endogenous substances and processes are those that originate from within a living system such as an organism, tissue, or cell.
In contrast, exogenous substances and processes are those that originate from outside of an organism.
For example, es ...
and external signals to regulate transcriptional activity throughout the day in a tissue-specific manner.
The circadian clock is intertwined with most cellular metabolic processes and it is affected by organism aging. The basic molecular mechanisms of the biological clock have been defined in
vertebrate
Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, ...
species, ''
Drosophila melanogaster
''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly" or "pomace fly". Starting with Ch ...
'',
plants
Plants are predominantly Photosynthesis, photosynthetic eukaryotes of the Kingdom (biology), kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all curr ...
,
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
,
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
,
and presumably also in
Archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
.
In 2017, the
Nobel Prize in Physiology or Medicine
The Nobel Prize in Physiology or Medicine is awarded yearly by the Nobel Assembly at the Karolinska Institute for outstanding discoveries in physiology or medicine. The Nobel Prize is not a single prize, but five separate prizes that, accord ...
was awarded to
Jeffrey C. Hall
Jeffrey Connor Hall (born May 3, 1945) is an American geneticist and Chronobiology, chronobiologist. Hall is Professor Emeritus of Biology at Brandeis University and currently resides in Cambridge, Maine.
Hall spent his career examining the neu ...
,
Michael Rosbash
Michael Morris Rosbash (born March 7, 1944) is an American geneticist and chronobiologist. Rosbash is a professor and researcher at Brandeis University and investigator at the Howard Hughes Medical Institute. Rosbash's research group cloned the ...
and
Michael W. Young
Michael Warren Young (born March 28, 1949) is an American biologist and geneticist. He has dedicated over three decades to research studying genetically controlled patterns of sleep and wakefulness within ''Drosophila melanogaster''.
At Rock ...
"for their discoveries of molecular mechanisms controlling the circadian rhythm" in fruit flies.
Vertebrate anatomy
In vertebrates, the master circadian clock is contained within the
suprachiasmatic nucleus
The suprachiasmatic nucleus or nuclei (SCN) is a tiny region of the brain in the hypothalamus, situated directly above the optic chiasm. It is responsible for controlling circadian rhythms. The neuronal and hormonal activities it generates regula ...
(SCN), a bilateral nerve cluster of about 20,000 neurons. The SCN itself is located in the
hypothalamus
The hypothalamus () is a part of the brain that contains a number of small nuclei with a variety of functions. One of the most important functions is to link the nervous system to the endocrine system via the pituitary gland. The hypothalamu ...
, a small region of the brain situated directly above the
optic chiasm
In neuroanatomy, the optic chiasm, or optic chiasma (; , ), is the part of the brain where the optic nerves cross. It is located at the bottom of the brain immediately inferior to the hypothalamus. The optic chiasm is found in all vertebrate ...
, where it receives input from specialized
photosensitive ganglion cell
Intrinsically photosensitive retinal ganglion cells (ipRGCs), also called photosensitive retinal ganglion cells (pRGC), or melanopsin-containing retinal ganglion cells (mRGCs), are a type of neuron in the retina of the mammalian eye. The presence ...
s in the retina via the
retinohypothalamic tract
In neuroanatomy, the retinohypothalamic tract (RHT) is a photic neural input pathway involved in the circadian rhythms of mammals. The origin of the retinohypothalamic tract is the intrinsically photosensitive retinal ganglion cells (ipRGC), whi ...
.
The SCN maintains control across the body by synchronizing "slave oscillators", which exhibit their own near-24-hour rhythms and control circadian phenomena in local tissue. Through intercellular signalling mechanisms such as
vasoactive intestinal peptide
Vasoactive intestinal peptide, also known as vasoactive intestinal polypeptide or VIP, is a peptide hormone that is vasoactive in the intestine. VIP is a peptide of 28 amino acid residues that belongs to a glucagon/secretin superfamily, the ligan ...
, the SCN signals other hypothalamic nuclei and the
pineal gland
The pineal gland, conarium, or epiphysis cerebri, is a small endocrine gland in the brain of most vertebrates. The pineal gland produces melatonin, a serotonin-derived hormone which modulates sleep, sleep patterns in both circadian rhythm, circ ...
to modulate
body temperature
Thermoregulation is the ability of an organism to keep its body temperature within certain boundaries, even when the surrounding temperature is very different. A thermoconforming organism, by contrast, simply adopts the surrounding temperature ...
and production of hormones such as
cortisol
Cortisol is a steroid hormone, in the glucocorticoid class of hormones. When used as a medication, it is known as hydrocortisone.
It is produced in many animals, mainly by the ''zona fasciculata'' of the adrenal cortex in the adrenal gland ...
and
melatonin
Melatonin is a natural product found in plants and animals. It is primarily known in animals as a hormone released by the pineal gland in the brain at night, and has long been associated with control of the sleep–wake cycle.
In vertebrates ...
; these hormones enter the
circulatory system
The blood circulatory system is a system of organs that includes the heart, blood vessels, and blood which is circulated throughout the entire body of a human or other vertebrate. It includes the cardiovascular system, or vascular system, tha ...
, and induce clock-driven effects throughout the organism.
It is not, however, clear precisely what signal (or signals) enacts principal entrainment to the many biochemical clocks contained in tissues throughout the body. See section "regulation of circadian oscillators" below for more details.
Transcriptional and non-transcriptional control
Evidence for a genetic basis of circadian rhythms in higher
eukaryote
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
s began with the discovery of the
period
Period may refer to:
Common uses
* Era, a length or span of time
* Full stop (or period), a punctuation mark
Arts, entertainment, and media
* Period (music), a concept in musical composition
* Periodic sentence (or rhetorical period), a concept ...
(''per'') locus in ''Drosophila melanogaster'' from forward genetic screens completed by
Ron Konopka
Ronald J. Konopka (1947-2015) was an American geneticist who studied chronobiology. He made his most notable contribution to the field while working with ''Drosophila'' in the lab of Seymour Benzer at the California Institute of Technology. Durin ...
and
Seymour Benzer
Seymour Benzer (October 15, 1921 – November 30, 2007) was an American physicist, molecular biologist and behavioral geneticist. His career began during the molecular biology revolution of the 1950s, and he eventually rose to prominence in the ...
in 1971.
Through the analysis of ''per'' circadian mutants and additional mutations on ''Drosophila'' clock genes, a model encompassing positive and negative autoregulatory
feedback
Feedback occurs when outputs of a system are routed back as inputs as part of a chain of cause-and-effect that forms a circuit or loop. The system can then be said to ''feed back'' into itself. The notion of cause-and-effect has to be handled ...
loops of
transcription
Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including:
Genetics
* Transcription (biology), the copying of DNA into RNA, the fir ...
and
translation
Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...
has been proposed. Core circadian 'clock' genes are defined as genes whose protein products are necessary components for the generation and regulation of circadian rhythms. Similar models have been suggested in mammals and other organisms.
Studies in cyanobacteria, however, changed our view of the clock mechanism, since it was found by Kondo and colleagues that these single-cell organisms could maintain accurate 24-hour timing in the absence of transcription, i.e. there was no requirement for a transcription-translation autoregulatory feedback loop for rhythms. Moreover, this clock was reconstructed in a test tube (i.e., in the absence of any cell components), proving that accurate 24-hour clocks can be formed without the need for genetic feedback circuits.
However, this mechanism was only applicable to cyanobacteria and not generic.
In 2011, a major breakthrough in understanding came from the
Reddy
Reddy (also transliterated as ''Raddi'', ''Reddi'', ''Reddiar'', ''Reddappa'', ''Reddy'') is a caste that originated in India, predominantly settled in Andhra Pradesh and Telangana. They are classified as a forward caste.
The origin of the ...
laboratory at the
University of Cambridge
, mottoeng = Literal: From here, light and sacred draughts.
Non literal: From this place, we gain enlightenment and precious knowledge.
, established =
, other_name = The Chancellor, Masters and Schola ...
. This group discovered circadian rhythms in redox proteins (
peroxiredoxins
Peroxiredoxins (Prxs, ; HGNC root symbol ''PRDX'') are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels and thereby mediate signal transduction in mammalian cells. The family members in humans are PRDX ...
) in cells that lacked a nucleus – human red blood cells. In these cells, there was no transcription or genetic circuits, and therefore no feedback loop. Similar observations were made in a marine alga and subsequently in mouse red blood cells. More importantly, redox oscillations as demonstrated by peroxiredoxin rhythms have now been seen in multiple distant kingdoms of life (eukaryotes, bacteria and archaea), covering the evolutionary tree.
Therefore, redox clocks look to be the grandfather clock, and genetic feedback circuits the major output mechanisms to control cell and tissue physiology and behavior.
Therefore, the model of the clock has to be considered as a product of an interaction between both transcriptional circuits and non-transcriptional elements such as redox oscillations and protein phosphorylation cycles.
Mammalian clocks
Selective
gene knockdown Gene knockdown is an experimental technique by which the expression of one or more of an organism's genes is reduced. The reduction can occur either through genetic modification or by treatment with a reagent such as a short DNA or RNA oligonucleot ...
of known components of the human circadian clock demonstrates both active compensatory mechanisms and redundancy are used to maintain function of the clock.
Several mammalian clock genes have been identified and characterized through experiments on animals harboring naturally occurring, chemically induced, and targeted knockout mutations, and various comparative genomic approaches.
The majority of identified clock components are transcriptional activators or repressors that modulate protein stability and nuclear translocation and create two interlocking feedback loops.
In the primary feedback loop, members of the
basic helix-loop-helix
BASIC (Beginners' All-purpose Symbolic Instruction Code) is a family of general-purpose, high-level programming languages designed for ease of use. The original version was created by John G. Kemeny and Thomas E. Kurtz at Dartmouth College ...
(bHLH)-PAS (Period-Arnt-Single-minded) transcription factor family,
CLOCK
A clock or a timepiece is a device used to measure and indicate time. The clock is one of the oldest human inventions, meeting the need to measure intervals of time shorter than the natural units such as the day, the lunar month and the ...
and
BMAL1
Aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL) or brain and muscle ARNT-Like 1 (BMAL1) is a protein that in humans is encoded by the gene on chromosome 11, region p15.3. It's also known as ''BMAL1'', ''MOP3'', and, less com ...
,
heterodimer
In biochemistry, a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. The word ''dimer'' has ...
ize in the cytoplasm to form a complex that, following translocation to the nucleus, initiates transcription of target genes such as the core clock genes 'period' genes (
PER1
The PER1 gene encodes the period circadian protein homolog 1 protein in humans.
Function
The PER1 protein is important to the maintenance of circadian rhythms in cells, and may also play a role in the development of cancer. This gene is a memb ...
,
PER2
PER2 is a protein in mammals encoded by the ''PER2'' gene. ''PER2'' is noted for its major role in circadian rhythms.
Discovery
The ''per ''gene'' ''was first discovered using forward genetics in ''Drosophila melanogaster, Drosophilla melanoga ...
, and
PER3
The PER3 gene encodes the period circadian protein homolog 3 protein in humans. PER3 is a paralog to the PER1 and PER2 genes. It is a circadian gene associate with delayed sleep phase syndrome in humans.
History
The Per3 gene was independently ...
) and two cryptochrome genes (
CRY1
Cryptochromes (from the Greek κρυπτός χρώμα, "hidden colour") are a class of flavoproteins found in plants and animals that are sensitive to blue light. They are involved in the circadian rhythms and the sensing of magnetic fields i ...
and
CRY2
Cryptochromes (from the Greek κρυπτός χρώμα, "hidden colour") are a class of flavoproteins found in plants and animals that are sensitive to blue light. They are involved in the circadian rhythms and the sensing of magnetic fields i ...
). Negative feedback is achieved by PER:CRY heterodimers that translocate back to the nucleus to repress their own transcription by inhibiting the activity of the CLOCK:BMAL1 complexes.
Another regulatory loop is induced when CLOCK:BMAL1 heterodimers activate the transcription of
Rev-ErbA
The Rev-Erb proteins are members of the nuclear receptor (NR) superfamily of intracellular transcription factors and key regulatory components of the circadian clock. There are two forms of the receptor, Rev-Erb alpha and Rev-Erb beta, wh ...
and Rora, two retinoic acid-related orphan nuclear receptors. REV-ERBa and RORa subsequently compete to bind
retinoic acid-related orphan receptor response elements (ROREs) present in Bmal1 promoter. Through the subsequent binding of ROREs, members of ROR and REV-ERB are able to regulate ''Bmal1''. While RORs activate transcription of ''Bmal1'', REV-ERBs repress the same transcription process. Hence, the circadian oscillation of ''Bmal1'' is both positively and negatively regulated by RORs and REV-ERBs.
Insect clocks
In ''D. melanogaster'', the gene cycle (CYC) is the orthologue of BMAL1 in mammals. Thus, CLOCK–CYC dimers activate the transcription of circadian genes. The gene timeless (TIM) is the orthologue for mammalian CRYs as the inhibitor; ''D. melanogaster'' CRY functions as a photoreceptor instead. In flies, CLK–CYC binds to the promoters of circadian-regulated genes only at the time of transcription. A stabilizing loop also exists where the gene vrille (VRI) inhibits whereas PAR-domain protein-1 (PDP1) activates Clock transcription.
Fungal clocks
In the filamentous fungus ''N. crassa'', the clock mechanism is analogous, but non-orthologous, to that of mammals and flies.
Plant clocks
The circadian clock in plants has completely different components to those in the animal, fungus, or bacterial clocks. The plant clock does have a conceptual similarity to the animal clock in that it consists of a series of interlocking transcriptional feedback loops. The genes involved in the clock show their peak expression at a fixed time of day. The first genes identified in the plant clock were
TOC1,
CCA1 and
LHY. The peak expression of the CCA1 and LHY genes occurs at dawn, and the peak expression of the TOC1 gene occurs roughly at dusk. CCA1/LHY and TOC1 proteins repress the expression of each other's genes. The result is that as CCA1/LHY protein levels start to reduce after dawn, it releases the repression on the TOC1 gene, allowing TOC1 expression and TOC1 protein levels to increase. As TOC1 protein levels increase, it further suppresses the expression of the CCA1 and LHY genes. The opposite of this sequence occurs overnight to re-establish the peak expression of CCA1 and LHY genes at dawn. There is much more complexity built into the clock, with multiple loops involving the PRR genes, the
Evening Complex and the light sensitive GIGANTIA and ZEITLUPE proteins.
Bacterial clocks
In
bacterial circadian rhythms Bacterial circadian rhythms, like other circadian rhythms, are endogenous "biological clocks" that have the following three characteristics: (a) in constant conditions (i.e. constant temperature and either constant light or constant darkness ) the ...
, the oscillations of the
phosphorylation
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
of
cyanobacterial
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue ...
Kai C protein was reconstituted in a cell free system (an ''in vitro'' clock) by incubating
KaiC
KaiC is a gene belonging to the KaiABC gene cluster (with KaiA, and KaiB) that, together, regulate bacterial circadian rhythms, specifically in cyanobacteria. KaiC encodes for the KaiC protein, which interacts with the KaiA and KaiB proteins in ...
with
KaiA Kaia or KAIA may refer to:
* Kaia (name), including a list of people with the name
* KaiA, a gene
* KAIA (group), a Filipino girl group
* KAIA (FM), radio station (91.5 FM) licensed to Blytheville, Arkansas, United States
* King Abdulaziz Internati ...
,
KaiB Kaib, KaiB, or KAIB may refer to:
* KAIB (FM), one of the radio stations of Air 1
* KaiB, a gene
* KAI Bandara, an Indonesian railway operator
* Korea Aviation Accident Investigation Board
* Rami Kaib
Rami Kaib (; born 8 May 1997) is a Tunisian ...
, and
ATP
ATP may refer to:
Companies and organizations
* Association of Tennis Professionals, men's professional tennis governing body
* American Technical Publishers, employee-owned publishing company
* ', a Danish pension
* Armenia Tree Project, non ...
.
Post-transcriptional modification
For a long time it was thought the transcriptional activation/repression cycles driven by the transcriptional regulators constituting the circadian clock was the main driving force for circadian gene expression in mammals. More recently, however, it was reported that only 22% of messenger RNA cycling genes are driven by de novo transcription.
RNA-level post-transcriptional mechanisms driving rhythmic protein expression were later reported, such as mRNA polyadenylation dynamics.
Fustin and co-workers identified methylation of internal adenosines (m
6A) within mRNA (notably of clock transcripts themselves) as a key regulator of the circadian period. Inhibition of m
6A methylation via pharmacological inhibition of cellular methylations or more specifically by siRNA-mediated silencing of the m
6A methylase ''Mettl3'' led to the dramatic elongation of the circadian period. In contrast, overexpression of ''Mettl3'' ''in vitro'' led to a shorter period. These observations clearly demonstrated the importance of RNA-level post-transcriptional regulation of the circadian clock, and concurrently established the physiological role of (m
6A) RNA methylation.
Post-translational modification
The autoregulatory feedback loops in clocks take about 24 hours to complete a cycle and constitute a circadian molecular clock. This generation of the ~24-hour molecular clock is governed by
post-translational modification
Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosome ...
s such as
phosphorylation
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
,
sumoylation
In molecular biology, SUMO (Small Ubiquitin-like Modifier) proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function. This process is called SUMOylation (sometimes w ...
,
histone acetylation
Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl-CoA to form ε-''N''-acetyllysine. DNA is wrapped around histones, and, by transferring an ...
and
methylation
In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These t ...
, and
ubiquitination
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
.
Reversible phosphorylation regulates important processes such as nuclear entry, formation of protein complexes and protein degradation. Each of these processes significantly contributes to keeping the period at ~24 hours and lends the precision of a circadian clock by affecting the stability of the aforementioned core clock proteins. Thus, while transcriptional regulation generates rhythmic RNA levels, regulated posttranslational modifications control protein abundance, subcellular localization, and repressor activity of PER and CRY.
Proteins responsible for post-translational modification of clock genes include
casein kinase
Casein kinase, a type of kinase enzyme, may refer to:
* Casein kinase 1, serine/threonine-selective protein kinase family
* Casein kinase 2
Casein kinase 2 ()(CK2/CSNK2) is a serine/threonine-selective protein kinase that has been implicated i ...
family members (
casein kinase 1 delta (CSNK1D) and
casein kinase 1 epsilon (CSNK1E) and the F-box
leucine-rich repeat protein 3 (FBXL3).
In mammals, CSNK1E and CSNK1D are critical factors that regulate the core circadian protein turnover.
Experimental manipulation on either of these proteins results in dramatic effects on circadian periods, such as altered kinase activities and cause shorter circadian periods, and further demonstrates the importance of the post-translational regulation within the core mechanism of the circadian clock.
These mutations have become of particular interest in humans as they are implicated in the
advanced sleep phase disorder
Advanced Sleep Phase Disorder (ASPD), also known as the advanced sleep-phase type (ASPT) of circadian rhythm sleep disorder, is a condition that is characterized by a recurrent pattern of early evening (e.g. 7-9 PM) sleepiness and very early mor ...
.
A small ubiquitin-related modifier protein modification of BMAL1 has also been proposed as another level of post-translational regulation.
Regulation of circadian oscillators
Circadian oscillators are simply oscillators with a period of approximately 24 hours. In response to light stimulus, the body corresponds with a system and network of pathways that work together to determine the biological day and night. The regulatory networks involved in keeping the clock precise span over a range of post-translation regulation mechanisms. Circadian oscillators may be regulated by
phosphorylation
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
, SUMOylation,
ubiquitination
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
, and
histone acetylation and deacetylation
In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn ar ...
, the covalent modification of the histone tail which controls the level of chromatin structures causing the gene to be expressed more readily.
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These t ...
of a protein structure adds a methyl group and regulates the protein function or gene expression and in histone methylation gene expression is either suppressed or activated through changing the DNA sequence. Histones go through an acetylation, methylation and phosphorylation process but the major structural and chemical changes happen when enzymes ''
histone acetyltransferase
Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl-CoA to form ε-''N''-acetyllysine. DNA is wrapped around histones, and, by transferring an ...
s'' (HAT) and ''
histone deacetylase
Histone deacetylases (, HDAC) are a class of enzymes that remove acetyl groups (O=C-CH3) from an ε-N-acetyl lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly. This is important because DNA is wrapped around his ...
s'' (HDAC) add or remove acetyl groups from the histone causing a major change in DNA expression. By changing DNA expression, histone acetylation and methylation regulate how the circadian oscillator operates. Fustin and co-workers provided a new layer of complexity to the regulation of circadian oscillator in mammals by showing that RNA methylation was necessary for efficient export of mature mRNA out of the nucleus: inhibition of RNA methylation caused nuclear retention of clock gene transcripts, leading to a longer circadian period.
A key feature of clocks is their ability to synchronize to external stimuli. The presence of cell-autonomous oscillators in almost every cell in the body raises the question of how these oscillators are temporally coordinated. The quest for universal timing cues for peripheral clocks in mammals has yielded principal entrainment signals such as feeding, temperature, and oxygen. Both feeding rhythms and temperature cycles were shown to synchronize peripheral clocks and even uncouple them from the master clock in the brain (e.g., daytime restricted feeding). Recently, oxygen rhythms were found to synchronize clocks in cultured cells.
Systems biology approaches to elucidate oscillating mechanisms
Modern experimental approaches using
systems biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...
have identified many novel components in biological clocks that suggest an integrative view on how organisms maintain circadian oscillation.
Recently, Baggs et al. developed a novel strategy termed "Gene Dosage Network Analysis" (GDNA) to describe network features in the human circadian clock that contribute to an organism's robustness against genetic perturbations.
In their study, the authors used
small interfering RNA
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20-24 (normally 21) base pairs in length, similar to miRNA, and operating wi ...
(siRNA) to induce dose-dependent changes in gene expression of clock components within immortalized human osteosarcoma U2OS cells in order to build gene association networks consistent with known biochemical constraints in the mammalian circadian clock. Employing multiple doses of siRNA powered their
quantitative PCR
A real-time polymerase chain reaction (real-time PCR, or qPCR) is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR). It monitors the amplification of a targeted DNA molecule during the PCR (i.e., in real ...
to uncover several network features of the circadian clock, including proportional responses of gene expression, signal propagation through interacting modules, and compensation through gene expression changes.
Proportional responses in downstream gene expression following
siRNA-induced perturbation revealed levels of expression that were actively altered with respect to the gene being knocked down. For example, when Bmal1 was knocked down in a dose-dependent manner,
Rev-ErbA alpha
Rev-Erb alpha (Rev-Erbɑ), also known as nuclear receptor subfamily 1 group D member 1 (NR1D1), is one of two Rev-Erb proteins in the nuclear receptor (NR) family of intracellular transcription factors. In humans, REV-ERBɑ is encoded by the '' ...
and
Rev-ErbA beta
Rev-Erb beta (Rev-Erbβ), also known as nuclear receptor subfamily 1 group D member 2 (NR1D2), is a member of the Rev-Erb protein family. Rev-Erbβ, like Rev-Erbα, belongs to the nuclear receptor superfamily of transcription factors and can mo ...
mRNA levels were shown to decrease in a linear, proportional manner. This supported previous findings that Bmal1 directly activates Rev-erb genes and further suggests Bmal1 as a strong contributor to Rev-erb expression.
In addition, the GDNA method provided a framework to study biological relay mechanisms in circadian networks through which modules communicate changes in gene expression.
The authors observed signal propagation through interactions between activators and repressors, and uncovered unidirectional paralog compensation among several clock gene repressors—for example, when
PER1
The PER1 gene encodes the period circadian protein homolog 1 protein in humans.
Function
The PER1 protein is important to the maintenance of circadian rhythms in cells, and may also play a role in the development of cancer. This gene is a memb ...
is depleted, there is an increase in Rev-erbs, which in turn propagates a signal to decrease expression in
BMAL1
Aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL) or brain and muscle ARNT-Like 1 (BMAL1) is a protein that in humans is encoded by the gene on chromosome 11, region p15.3. It's also known as ''BMAL1'', ''MOP3'', and, less com ...
, the target of the Rev-erb repressors.
By examining the knockdown of several transcriptional repressors, GDNA also revealed paralog compensation where gene paralogs were upregulated through an active mechanism by which gene function is replaced following knockdown in a non-redundant manner—that is, one component is sufficient to sustain function. These results further suggested that a clock network utilizes active compensatory mechanisms rather than simple redundancy to confer robustness and maintain function. In essence, the authors proposed that the observed network features act in concert as a genetic buffering system to maintain clock function in the face of genetic and environmental perturbation.
Following this logic, we may use
genomics
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
to explore network features in the circadian oscillator.
Another study conducted by Zhang et al. also employed a genome-wide
small interfering RNA
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20-24 (normally 21) base pairs in length, similar to miRNA, and operating wi ...
screen in U2OS cell line to identify additional clock genes and modifiers using luciferase reporter gene expression.
Knockdown of nearly 1000 genes reduced rhythm amplitude. The authors found and confirmed hundreds of potent effects on
period
Period may refer to:
Common uses
* Era, a length or span of time
* Full stop (or period), a punctuation mark
Arts, entertainment, and media
* Period (music), a concept in musical composition
* Periodic sentence (or rhetorical period), a concept ...
length or increased amplitude in secondary screens. Characterization of a subset of these genes demonstrated a dosage-dependent effect on
oscillator
Oscillation is the repetitive or periodic variation, typically in time, of some measure about a central value (often a point of equilibrium) or between two or more different states. Familiar examples of oscillation include a swinging pendulum ...
function. Protein interaction network analysis showed that dozens of gene products were directly or indirectly associate with known clock components. Pathway analysis revealed these genes are overrepresented for components of
insulin
Insulin (, from Latin ''insula'', 'island') is a peptide hormone produced by beta cells of the pancreatic islets encoded in humans by the ''INS'' gene. It is considered to be the main anabolic hormone of the body. It regulates the metabolism o ...
and
hedgehog signaling pathway
The Hedgehog signaling pathway is a signaling pathway that transmits information to embryonic cells required for proper cell differentiation. Different parts of the embryo have different concentrations of hedgehog signaling proteins. The pathwa ...
, the
cell cycle
The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication) and some of its organelles, and subs ...
, and folate metabolism. Coupled with data demonstrating that many of these pathways are clock-regulated, Zhang et al. postulated that the clock is interconnected with many aspects of cellular function.
A
systems biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...
approach may relate circadian rhythms to cellular phenomena that were not originally considered regulators of circadian oscillation. For example, a 2014 workshop
at
NHLBI
The National Heart, Lung, and Blood Institute (NHLBI) is the third largest Institute of the National Institutes of Health, located in Bethesda, Maryland, United States. It is tasked with allocating about $3.6 billion in FY 2020 in tax revenue to ...
assessed newer circadian genomic findings and discussed the interface between the body clock and many different cellular processes.
Variation in circadian clocks
While a precise 24-hour circadian clock is found in many organisms, it is not universal. Organisms living in the high arctic or high antarctic do not experience solar time in all seasons, though most are believed to maintain a circadian rhythm close to 24 hours, such as bears during torpor.
Much of the earth's biomass resides in the dark biosphere, and while these organisms may exhibit rhythmic physiology, for these organisms the dominant rhythm is unlikely to be circadian.
For east-west migratory organisms—and especially those organisms that circumnavigate the globe—the absolute 24-hour phase might deviate over months, seasons, or years.
Some spiders exhibit unusually long or short circadian clocks. Some
trashline orbweavers, for example, have 18.5-hour circadian clocks, but are still able to entrain to a 24-hour cycle. This adaptation may help the spiders avoid predators by allowing them to be most active before sunrise.
Black widows' clocks are arrhythmic, perhaps due to their preference for dark environments.
See also
*
Chemical clock
A chemical clock (or clock reaction) is a complex mixture of reacting chemical compounds in which the onset of an observable property (discoloration or coloration) occurs after a predictable induction time due to the presence of clock species at a ...
*
Chemical oscillator
A chemical oscillator is a complex mixture of reacting chemical compounds in which the concentration of one or more components exhibits periodic changes. They are a class of reactions that serve as an example of non-equilibrium thermodynamics with ...
References
External links
Circadian screen search
{{DEFAULTSORT:Circadian clock
Circadian rhythm
Oscillation