Editing Circadian clock (section)

== Transcriptional and non-transcriptional control ==
Evidence for a genetic basis of circadian rhythms in higher [[eukaryote]]s began with the discovery of the [[period (gene)|period]] (''per'') locus in ''Drosophila melanogaster'' from forward genetic screens completed by [[Ron Konopka]] and [[Seymour Benzer]] in 1971.<ref name="pmid5002428">{{cite journal | vauthors = Konopka RJ, Benzer S | title = Clock mutants of Drosophila melanogaster | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 68 | issue = 9 | pages = 2112–2116 | date = September 1971 | pmid = 5002428 | pmc = 389363 | doi = 10.1073/pnas.68.9.2112 | doi-access = free | bibcode = 1971PNAS...68.2112K }}</ref> Through the analysis of ''per'' circadian mutants and additional mutations on ''Drosophila'' clock genes, a model encompassing positive and negative autoregulatory [[feedback]] loops of [[transcription (genetics)|transcription]] and [[Translation (biology)|translation]] 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.<ref name="pmid6440029">{{cite journal | vauthors = Bargiello TA, Jackson FR, Young MW | title = Restoration of circadian behavioural rhythms by gene transfer in Drosophila | journal = Nature | volume = 312 | issue = 5996 | pages = 752–754 | year = 1984 | pmid = 6440029 | doi = 10.1038/312752a0 | s2cid = 4259316 | bibcode = 1984Natur.312..752B }}</ref><ref name="pmid10807566">{{cite journal | vauthors = Shearman LP, Sriram S, Weaver DR, Maywood ES, Chaves I, Zheng B, Kume K, Lee CC, van der Horst GT, Hastings MH, Reppert SM | display-authors = 6 | title = Interacting molecular loops in the mammalian circadian clock | journal = Science | volume = 288 | issue = 5468 | pages = 1013–1019 | date = May 2000 | pmid = 10807566 | doi = 10.1126/science.288.5468.1013 | bibcode = 2000Sci...288.1013S }}</ref>

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.<ref>{{cite journal | vauthors = Tomita J, Nakajima M, Kondo T, Iwasaki H | title = No transcription-translation feedback in circadian rhythm of KaiC phosphorylation | journal = Science | volume = 307 | issue = 5707 | pages = 251–254 | date = January 2005 | pmid = 15550625 | doi = 10.1126/science.1102540 | s2cid = 9447128 | bibcode = 2005Sci...307..251T | doi-access = free }}</ref> 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.<ref name="pmid15831759"/> However, this mechanism was only applicable to cyanobacteria and not generic.

In 2011, a major breakthrough in understanding came from the [[Akhilesh Reddy|Reddy]] laboratory at the [[University of Cambridge]]. This group discovered circadian rhythms in redox proteins ([[peroxiredoxins]]) in cells that lacked a nucleus – human red blood cells.<ref>{{cite journal | vauthors = O'Neill JS, Reddy AB | title = Circadian clocks in human red blood cells | journal = Nature | volume = 469 | issue = 7331 | pages = 498–503 | date = January 2011 | pmid = 21270888 | pmc = 3040566 | doi = 10.1038/nature09702 | bibcode = 2011Natur.469..498O }}</ref> In these cells, there was no transcription or genetic circuits, and therefore no feedback loop. Similar observations were made in a marine alga<ref>{{cite journal | vauthors = O'Neill JS, van Ooijen G, Dixon LE, Troein C, Corellou F, Bouget FY, Reddy AB, Millar AJ | display-authors = 6 | title = Circadian rhythms persist without transcription in a eukaryote | journal = Nature | volume = 469 | issue = 7331 | pages = 554–558 | date = January 2011 | pmid = 21270895 | pmc = 3040569 | doi = 10.1038/nature09654 | bibcode = 2011Natur.469..554O }}</ref> and subsequently in mouse red blood cells.<ref>{{cite journal | vauthors = Cho CS, Yoon HJ, Kim JY, Woo HA, Rhee SG | title = Circadian rhythm of hyperoxidized peroxiredoxin II is determined by hemoglobin autoxidation and the 20S proteasome in red blood cells | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 33 | pages = 12043–12048 | date = August 2014 | pmid = 25092340 | pmc = 4142998 | doi = 10.1073/pnas.1401100111 | doi-access = free | bibcode = 2014PNAS..11112043C }}</ref> 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.<ref name="Edgar_2012"/><ref>{{cite journal | vauthors = Olmedo M, O'Neill JS, Edgar RS, Valekunja UK, Reddy AB, Merrow M | title = Circadian regulation of olfaction and an evolutionarily conserved, nontranscriptional marker in Caenorhabditis elegans | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 109 | issue = 50 | pages = 20479–20484 | date = December 2012 | pmid = 23185015 | pmc = 3528576 | doi = 10.1073/pnas.1211705109 | doi-access = free | bibcode = 2012PNAS..10920479O }}</ref> 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.<ref>{{cite web| vauthors = MacKenzie D |title=Biological clock began ticking 2.5 billion years ago | url = https://www.newscientist.com/article/mg21428653.900-biological-clock-began-ticking-25-billion-years-ago.html|website=New Scientist}}</ref><ref>{{cite journal | vauthors = Loudon AS | title = Circadian biology: a 2.5 billion year old clock | journal = Current Biology | volume = 22 | issue = 14 | pages = R570–R571 | date = July 2012 | pmid = 22835791 | doi = 10.1016/j.cub.2012.06.023 | doi-access = free }}</ref>

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.<ref>{{cite journal | vauthors = Reddy AB, Rey G | title = Metabolic and nontranscriptional circadian clocks: eukaryotes | journal = Annual Review of Biochemistry | volume = 83 | pages = 165–189 | date = 2014 | pmid = 24606143 | pmc = 4768355 | doi = 10.1146/annurev-biochem-060713-035623 }}</ref><ref>{{cite journal | vauthors = Qin X, Byrne M, Xu Y, Mori T, Johnson CH | title = Coupling of a core post-translational pacemaker to a slave transcription/translation feedback loop in a circadian system | journal = PLOS Biology | volume = 8 | issue = 6 | pages = e1000394 | date = June 2010 | pmid = 20563306 | pmc = 2885980 | doi = 10.1371/journal.pbio.1000394 | doi-access = free }}</ref>

=== Mammalian clocks ===
Selective [[gene knockdown]] of known components of the human circadian clock demonstrates both active compensatory mechanisms and redundancy are used to maintain function of the clock.<ref name="Walton">{{cite journal | vauthors = Walton ZE, Altman BJ, Brooks RC, Dang CV |title=Circadian Clock's Cancer Connections |journal=Annual Review of Cancer Biology |date=4 March 2018 |volume=2 |issue=1 |pages=133–153 |doi=10.1146/annurev-cancerbio-030617-050216 |s2cid=91120424 |language=en |issn=2472-3428|doi-access=free }}</ref><ref name="Zhang">{{cite journal | vauthors = Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW, Janes J, Su AI, Hogenesch JB, Kay SA | display-authors = 6 | title = A genome-wide RNAi screen for modifiers of the circadian clock in human cells | journal = Cell | volume = 139 | issue = 1 | pages = 199–210 | date = October 2009 | pmid = 19765810 | pmc = 2777987 | doi = 10.1016/j.cell.2009.08.031 }}</ref><ref name="Baggs">{{cite journal | vauthors = Baggs JE, Price TS, DiTacchio L, Panda S, Fitzgerald GA, Hogenesch JB | title = Network features of the mammalian circadian clock | journal = PLOS Biology | volume = 7 | issue = 3 | pages = e52 | date = March 2009 | pmid = 19278294 | pmc = 2653556 | doi = 10.1371/journal.pbio.1000052 | veditors = Schibler U | doi-access = free }}</ref><ref>{{cite journal | vauthors = Brancaccio M, Edwards MD, Patton AP, Smyllie NJ, Chesham JE, Maywood ES, Hastings MH | title = Cell-autonomous clock of astrocytes drives circadian behavior in mammals | journal = Science | volume = 363 | issue = 6423 | pages = 187–192 | date = January 2019 | pmid = 30630934 | pmc = 6440650 | doi = 10.1126/science.aat4104 | bibcode = 2019Sci...363..187B }}</ref>
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.<ref name="Walton"/>

The majority of identified clock components are transcriptional activators or repressors that modulate protein stability and nuclear translocation and create two interlocking [[feedback loops]].<ref name="Ko">{{cite journal | vauthors = Ko CH, Takahashi JS | title = Molecular components of the mammalian circadian clock | journal = Human Molecular Genetics | volume = 15 | issue = Spec No 2 | pages = R271–R277 | date = October 2006 | pmid = 16987893 | doi = 10.1093/hmg/ddl207 | doi-access = free | pmc = 3762864 }}</ref> In the primary feedback loop, members of the [[basic helix-loop-helix]] (bHLH)-PAS (Period-Arnt-Single-minded) transcription factor family, [[CLOCK]] and [[ARNTL|BMAL1]], [[heterodimer]]ize in the cytoplasm to form a complex that, following translocation to the [[Cell nucleus|nucleus]], initiates transcription of target genes such as the core clock genes 'period' genes ([[PER1]], [[PER2]], and [[PER3]]) and two cryptochrome genes ([[CRY1]] and [[CRY2]]). [[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.<ref name="Lowrey"/> Another regulatory loop is induced when CLOCK:BMAL1 heterodimers activate the transcription of [[Rev-ErbA]] and Rora, two retinoic acid-related orphan nuclear receptors. REV-ERBa and RORa subsequently compete to bind Retinoid-related orphan receptor response element|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.<ref name="Ko"/>

=== 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.<ref name="Gallego">{{cite journal | vauthors = Gallego M, Virshup DM | title = Post-translational modifications regulate the ticking of the circadian clock | journal = Nature Reviews. Molecular Cell Biology | volume = 8 | issue = 2 | pages = 139–148 | date = February 2007 | pmid = 17245414 | doi = 10.1038/nrm2106 | s2cid = 27163437 }}</ref>

=== Fungal clocks ===
In the filamentous fungus ''N. crassa'', the clock mechanism is analogous, but non-orthologous, to that of mammals and flies.<ref name="pmid16651653">{{cite journal | vauthors = Brunner M, Schafmeier T | title = Transcriptional and post-transcriptional regulation of the circadian clock of cyanobacteria and Neurospora | journal = Genes & Development | volume = 20 | issue = 9 | pages = 1061–1074 | date = May 2006 | pmid = 16651653 | doi = 10.1101/gad.1410406 | doi-access = free }}</ref>

=== 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 (gene)|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 [[ELF4|Evening Complex]] and the light sensitive GIGANTIA and ZEITLUPE proteins.

=== Bacterial clocks ===
In [[bacterial circadian rhythms]], the oscillations of the [[phosphorylation]] of [[cyanobacterial]] Kai C protein was reconstituted in a cell free system (an ''in vitro'' clock) by incubating [[KaiC]] with [[KaiA]], [[KaiB]], and [[Adenosine triphosphate|ATP]].<ref name="pmid15831759">{{cite journal | vauthors = Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T | display-authors = 6 | title = Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro | journal = Science | volume = 308 | issue = 5720 | pages = 414–415 | date = April 2005 | pmid = 15831759 | doi = 10.1126/science.1108451 | url = http://pdfs.semanticscholar.org/67a0/b846f759656e200d0470b82e2af25d3a392a.pdf | url-status = dead | s2cid = 24833877 | bibcode = 2005Sci...308..414N | archive-url = https://web.archive.org/web/20190225201107/http://pdfs.semanticscholar.org/67a0/b846f759656e200d0470b82e2af25d3a392a.pdf | archive-date = 2019-02-25 }}</ref>