Editing Circadian rhythm (section)

==In plants==
<!-- Deleted image removed: [[File:TOC1 interactions.jpg|thumb|Illustration of the morning (yellow) and evening (gray) circadian clock loops in
''Arabidopsis'', entrainable through light. Transcriptional regulation is shown through black lines and protein complexes are denoted by dashed black lines. Post-translational regulation is shown by dashed red lines. Light sensitive elements are denoted with lightning bolts and yellow circles.]] -->
[[File:Jungpflanze des Seidenbaums (Schlafbaum).png|thumb|Sleeping tree by day and night]]
Plant circadian rhythms tell the plant what season it is and when to flower for the best chance of attracting pollinators. Behaviors showing rhythms include leaf movement ([[Nyctinasty]]), growth, germination, stomatal/gas exchange, [[enzyme activity]], [[Photosynthesis|photosynthetic]] activity, and fragrance emission, among others.<ref name=webb03>{{cite journal | vauthors = Webb AA | title = The physiology of circadian rhythms in plants | journal = The New Phytologist | volume = 160 | issue = 2 | pages = 281–303 | date = November 2003 | pmid = 33832173 | doi = 10.1046/j.1469-8137.2003.00895.x | s2cid = 15688409 | jstor = 1514280 | doi-access = free | bibcode = 2003NewPh.160..281W }}</ref> Circadian rhythms occur as a plant entrains to synchronize with the light cycle of its surrounding environment. These rhythms are [[endogenous]]ly generated, self-sustaining and are relatively constant over a range of ambient temperatures. Important features include two interacting [[Transcription translation feedback loop|transcription-translation feedback loops]]: [[protein]]s containing PAS domains, which facilitate protein-protein interactions; and several photoreceptors that fine-tune the clock to different light conditions. Anticipation of changes in the environment allows appropriate changes in a plant's physiological state, conferring an adaptive advantage.<ref name=mcclung06>{{cite journal | vauthors = McClung CR | title = Plant circadian rhythms | journal = The Plant Cell | volume = 18 | issue = 4 | pages = 792–803 | date = April 2006 | pmid = 16595397 | pmc = 1425852 | doi = 10.1105/tpc.106.040980 | bibcode = 2006PlanC..18..792M }}</ref> A better understanding of plant circadian rhythms has applications in agriculture, such as helping farmers stagger crop harvests to extend crop availability and securing against massive losses due to weather.

Light is the signal by which plants synchronize their internal clocks to their environment and is sensed by a wide variety of photoreceptors. Red and blue light are absorbed through several [[phytochrome]]s and [[cryptochrome]]s. Phytochrome A, phyA, is light labile and allows germination and de-etiolation when light is scarce.<ref>{{cite journal | vauthors = Legris M, Ince YÇ, Fankhauser C | title = Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants | journal = Nature Communications | volume = 10 | issue = 1 | pages = 5219 | date = November 2019 | pmid = 31745087 | pmc = 6864062 | doi = 10.1038/s41467-019-13045-0 | bibcode = 2019NatCo..10.5219L }}</ref> Phytochromes B–E are more stable with {{Not a typo|phyB}}, the main phytochrome in seedlings grown in the light. The cryptochrome (cry) gene is also a light-sensitive component of the circadian clock and is thought to be involved both as a photoreceptor and as part of the clock's endogenous pacemaker mechanism. Cryptochromes 1–2 (involved in blue–UVA) help to maintain the period length in the clock through a whole range of light conditions.<ref name=webb03/><ref name=mcclung06/>
[[File:Data on circadian rhythm of gene expression in four seedlings. Two of these Arabidopsis thaliana seedlings carry a firefly luciferase reporter for transcription of the gene CCA1 and two for TOC1.png|alt=Graph showing two pairs of rhythmic timeseries, peaking at alternating times of day, over six, 24-hour cycles.|thumb|Graph showing timeseries data from [[bioluminescence imaging]] of circadian reporter genes. [[Genetically modified organism|Transgenic]] seedlings of ''[[Arabidopsis thaliana]]'' were imaged by a cooled [[Charge-coupled device|CCD camera]] under three cycles of 12h light: 12h dark followed by 3 days of constant light (from 96h). Their genomes carry firefly [[luciferase]] [[reporter gene]]s driven by the promoter sequences of clock genes. The signals of seedlings 61 (red) and 62 (blue) reflect transcription of the gene [[Circadian Clock Associated 1|CCA1]], peaking after lights-on (48h, 72h, etc.). Seedlings 64 (pale grey) and 65 (teal) reflect [[TOC1 (gene)|TOC1]], peaking before lights-off (36h, 60h, etc.). The timeseries show 24-hour, circadian rhythms of gene expression in the living plants.]]
The central oscillator generates a self-sustaining rhythm and is driven by two interacting feedback loops that are active at different times of day. The morning loop consists of [[CCA1]] (Circadian and Clock-Associated 1) and [[LHY]] (Late Elongated Hypocotyl), which encode closely related [[MYB (gene)|MYB transcription factors]] that regulate circadian rhythms in ''Arabidopsis'', as well as [[Pseudo-response regulator|PRR 7 and 9]] (Pseudo-Response Regulators.)  The evening loop consists of GI (Gigantea) and ELF4, both involved in regulation of flowering time genes.<ref name=Mizoguchi>{{cite journal | vauthors = Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K, Onouchi H, Mouradov A, Fowler S, Kamada H, Putterill J, Coupland G | title = Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis | journal = The Plant Cell | volume = 17 | issue = 8 | pages = 2255–2270 | date = August 2005 | pmid = 16006578 | pmc = 1182487 | doi = 10.1105/tpc.105.033464 | bibcode = 2005PlanC..17.2255M }}</ref><ref>{{cite journal | vauthors = Kolmos E, Davis SJ | title = ELF4 as a Central Gene in the Circadian Clock | journal = Plant Signaling & Behavior | volume = 2 | issue = 5 | pages = 370–372 | date = September 2007 | pmid = 19704602 | pmc = 2634215 | doi = 10.4161/psb.2.5.4463 | bibcode = 2007PlSiB...2..370K }}</ref> When CCA1 and LHY are overexpressed (under constant light or dark conditions), plants become arrhythmic, and mRNA signals reduce, contributing to a [[negative feedback]] loop. Gene expression of CCA1 and LHY oscillates and peaks in the early morning, whereas [[TOC1 gene]] expression oscillates and peaks in the early evening. While it was previously hypothesised that these three genes model a negative feedback loop in which over-expressed CCA1 and LHY repress TOC1 and over-expressed TOC1 is a positive regulator of CCA1 and LHY,<ref name=mcclung06/> it was shown in 2012 by Andrew Millar and others that TOC1, in fact, serves as a repressor not only of CCA1, LHY, and PRR7 and 9 in the morning loop but also of GI and ELF4 in the evening loop. This finding and further computational modeling of [[TOC1 gene]] functions and interactions suggest a reframing of the plant circadian clock as a triple negative-component [[repressilator]] model rather than the positive/negative-element feedback loop characterizing the clock in mammals.<ref>{{cite journal | vauthors = Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ | title = The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops | journal = Molecular Systems Biology | volume = 8 | pages = 574 | date = March 2012 | pmid = 22395476 | pmc = 3321525 | doi = 10.1038/msb.2012.6 }}</ref>

In 2018, researchers found that the expression of PRR5 and TOC1 hnRNA nascent transcripts follows the same oscillatory pattern as processed mRNA transcripts rhythmically in ''A. thaliana''. LNKs binds to the 5'region of PRR5 and TOC1 and interacts with RNAP II and other transcription factors. Moreover, RVE8-LNKs interaction enables a permissive histone-methylation pattern (H3K4me3) to be modified and the histone-modification itself parallels the oscillation of clock gene expression.<ref>{{cite journal | vauthors = Ma Y, Gil S, Grasser KD, Mas P | title = Targeted Recruitment of the Basal Transcriptional Machinery by LNK Clock Components Controls the Circadian Rhythms of Nascent RNAs in Arabidopsis | journal = The Plant Cell | volume = 30 | issue = 4 | pages = 907–924 | date = April 2018 | pmid = 29618629 | pmc = 5973845 | doi = 10.1105/tpc.18.00052 | bibcode = 2018PlanC..30..907M }}</ref>

It has previously been found that matching a plant's circadian rhythm to its external environment's light and dark cycles has the potential to positively affect the plant.<ref name=":02">{{cite journal | vauthors = Dodd AN, Salathia N, Hall A, Kévei E, Tóth R, Nagy F, Hibberd JM, Millar AJ, Webb AA | title = Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage | journal = Science | volume = 309 | issue = 5734 | pages = 630–633 | date = July 2005 | pmid = 16040710 | doi = 10.1126/science.1115581 | s2cid = 25739247 | bibcode = 2005Sci...309..630D }}</ref> Researchers came to this conclusion by performing experiments on three different varieties of ''[[Arabidopsis thaliana]]''. One of these varieties had a normal 24-hour circadian cycle.<ref name=":02" /> The other two varieties were mutated, one to have a circadian cycle of more than 27 hours, and one to have a shorter than normal circadian cycle of 20 hours.<ref name=":02" />

The ''Arabidopsis'' with the 24-hour circadian cycle was grown in three different environments.<ref name=":02" /> One of these environments had a 20-hour light and dark cycle (10 hours of light and 10 hours of dark), the other had a 24-hour light and dark cycle (12 hours of light and 12 hours of dark),and the final environment had a 28-hour light and dark cycle (14 hours of light and 14 hours of dark).<ref name=":02" /> The two mutated plants were grown in both an environment that had a 20-hour light and dark cycle and in an environment that had a 28-hour light and dark cycle.<ref name=":02" /> It was found that the variety of ''Arabidopsis'' with a 24-hour circadian rhythm cycle grew best in an environment that also had a 24-hour light and dark cycle.<ref name=":02" /> Overall, it was found that all the varieties of ''Arabidopsis thaliana'' had greater levels of [[chlorophyll]] and increased growth in environments whose light and dark cycles matched their circadian rhythm.<ref name=":02" />

Researchers suggested that a reason for this could be that matching an ''Arabidopsis''{{'s}} circadian rhythm to its environment could allow the plant to be better prepared for dawn and dusk, and thus be able to better synchronize its processes.<ref name=":02" /> In this study, it was also found that the genes that help to control chlorophyll peaked a few hours after dawn.<ref name=":02" /> This appears to be consistent with the proposed phenomenon known as metabolic dawn.<ref name=":1">{{cite journal | vauthors = Dodd AN, Belbin FE, Frank A, Webb AA | title = Interactions between circadian clocks and photosynthesis for the temporal and spatial coordination of metabolism | journal = Frontiers in Plant Science | volume = 6 | pages = 245 | year = 2015 | pmid = 25914715 | pmc = 4391236 | doi = 10.3389/fpls.2015.00245 | doi-access = free | bibcode = 2015FrPS....6..245D }}</ref>

According to the metabolic dawn hypothesis, sugars produced by photosynthesis have potential to help regulate the circadian rhythm and certain photosynthetic and metabolic pathways.<ref name=":1" /><ref>{{cite journal | vauthors = Webb AA, Seki M, Satake A, Caldana C | title = Continuous dynamic adjustment of the plant circadian oscillator | journal = Nature Communications | volume = 10 | issue = 1 | pages = 550 | date = February 2019 | pmid = 30710080 | pmc = 6358598 | doi = 10.1038/s41467-019-08398-5 | bibcode = 2019NatCo..10..550W }}</ref> As the sun rises, more light becomes available, which normally allows more photosynthesis to occur.<ref name=":1" /> The sugars produced by photosynthesis repress PRR7.<ref name=":2">{{cite journal | vauthors = Haydon MJ, Mielczarek O, Robertson FC, Hubbard KE, Webb AA | title = Photosynthetic entrainment of the Arabidopsis thaliana circadian clock | journal = Nature | volume = 502 | issue = 7473 | pages = 689–692 | date = October 2013 | pmid = 24153186 | pmc = 3827739 | doi = 10.1038/nature12603 | bibcode = 2013Natur.502..689H }}</ref> This repression of PRR7 then leads to the increased expression of CCA1.<ref name=":2" /> On the other hand, decreased photosynthetic sugar levels increase PRR7 expression and decrease CCA1 expression.<ref name=":1" /> This feedback loop between CCA1 and PRR7 is what is proposed to cause metabolic dawn.<ref name=":1" /><ref>{{cite journal | vauthors = Farré EM, Kay SA | title = PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis | journal = The Plant Journal | volume = 52 | issue = 3 | pages = 548–560 | date = November 2007 | pmid = 17877705 | doi = 10.1111/j.1365-313X.2007.03258.x | doi-access = free }}</ref>