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Bacterial circadian rhythm

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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 {LL} or constant darkness {DD}) they oscillate with a period that is close to, but not exactly, 24 hours in duration, (b) this "free-running" rhythm is temperature compensated, and (c) the rhythm will entrain to an appropriate environmental cycle.

Until the mid-1980s, it was thought that only eukaryotic cells had circadian rhythms. It is now known that cyanobacteria (a phylum of photosynthetic eubacteria) have well-documented circadian rhythms that meet all the criteria of bona fide circadian rhythms. In these bacteria, three key proteins whose structures have been determined, KaiA, KaiB, and KaiC can form a molecular clockwork that orchestrates global gene expression.[1] This system enhances the fitness of cyanobacteria in rhythmic environments.

History: are prokaryotes capable of circadian rhythmicity?

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Before the mid-1980s, it was believed that only eukaryotes had circadian systems.[2]

 
Time-lapse video of circadian luminescence rhythms from cyanobacterial colonies on a petri dish. Each spot is a single cyanobacterial colony.

In 1985–6, several research groups discovered that cyanobacteria display daily rhythms of nitrogen fixation in both light/dark (LD) cycles and in constant light. The group of Huang and co-workers was the first to recognize clearly that the cyanobacterium Synechococcus sp. RF-1 was exhibiting circadian rhythms, and in a series of publications beginning in 1986 demonstrated all three of the salient characteristics of circadian rhythms described above in the same organism, the unicellular freshwater Synechococcus sp. RF-1.[3][4] Another ground-breaking study was that of Sweeney and Borgese.[5]

Inspired by the research of the aforementioned pioneers, the collaborative group of Takao Kondo, Carl H. Johnson, Susan Golden, and Masahiro Ishiura genetically transformed the cyanobacterium Synechococcus elongatus with a luciferase reporter that allowed rhythmic gene expression to be assayed non-invasively as rhythmically "glowing" cells.[6][7] This system allowed an exquisitely precise circadian rhythm of luminescence to be measured from cell populations[6] and even from single cyanobacterial cells.[8] The figure shows the daily oscillations in luminescence of many individual cyanobacterial colonies on a petri dish; note the synchrony of rhythmicity among the various colonies.

Relationship to cell division

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Despite predictions that circadian clocks would not be expressed by cells that are doubling faster than once per 24 hours,[9] the cyanobacterial rhythms continue in cultures that are growing with doubling times as rapid as one division every 5–6 hours.[10][11][12]

Adaptive significance

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Adaptive advantage of cyanobacterial circadian clock

Do circadian timekeepers enhance the fitness of organisms growing under natural conditions? Circadian clocks are assumed to enhance the fitness of organisms by improving their ability to predict and anticipate daily cycles in environmental factors. However, there have been few rigorous tests of this proposition in any organism. [13] Cyanobacteria are one of the few organisms in which such a test has been performed. The adaptive fitness test was done by mixing cyanobacterial strains that express different circadian properties (i.e., rhythmicity vs. arhythmicity, different periods, etc.) and growing them in competition under different environmental conditions. The idea was to determine if having an appropriately functional clock system enhances fitness under competitive conditions. The result was that strains with a functioning biological clock out-compete arhythmic strains in environments that have a rhythmic light/dark cycle (e.g., 12 hours of light alternating with 12 hours of darkness), whereas in "constant" environments (e.g., constant illumination) rhythmic and arhythmic strains grow at comparable rates.[14] Among rhythmic strains with different periods, the strains whose endogenous period most closely matches the period of the environmental cycle is able to out-compete strains whose period does not match that of the environment.[15] Similar results were later obtained in plants[16] and mice.[17]

Global regulation of gene expression and chromosomal topology

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In eukaryotes, about 10–20% of the genes are rhythmically expressed (as gauged by rhythms of mRNA abundance). However, in cyanobacteria, a much larger percentage of genes are controlled by the circadian clock. For example, one study has shown that the activity of essentially all promoters in the genome are rhythmically regulated.[18] The mechanism by which this global gene regulation is mechanistically linked to the circadian clock appears to be due to clock triggering of a transcriptional cascade[19][20] coupled to rhythmic changes in the topology of the entire cyanobacterial chromosome.[21][22]

Molecular mechanism of the cyanobacterial clockwork

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Time-lapse video of cyanobacterial clock mutants with different periods. The circadian rhythm of luminescence from four different strains in constant light are shown: Wild-type (top) with a period of about 25 h, a long-period mutant (second from top) with a period of about 50 h, a short-period mutant (third from top) with a period of about 17 h, and an arhythmic mutant (bottom).

The S. elongatus luciferase reporter system was used to screen for clock gene mutants, of which many were isolated.[23] The figure shows a few of the many mutants that were discovered. These mutants were used to identify the core KaiA, KaiB, KaiC clock genes.[1]

At first, the cyanobacterial clockwork appeared to be a transcription and translation feedback loop in which clock proteins autoregulate the activity of their own promoters by a process that was similar in concept to the circadian clock loops of eukaryotes.[1][24] Subsequently, however, several lines of evidence indicated that transcription and translation was not necessary for circadian rhythms of Kai proteins,[25][26][27] the most spectacular being that the three purified Kai proteins can reconstitute a temperature-compensated circadian oscillation in a test tube.[28]

In vivo, the output of this biochemical KaiABC oscillator to rhythms of gene expression appears to be mediated by KaiC phosphorylation status (see below) regulating a biochemical cascade involving a histidine kinase SasA and a phosphatase CikA that activate/inactivate the globally acting transcription factor RpaA.[19][20] A contributing factor to the global transcription programs is rhythms of chromosomal topology in which the circadian clock orchestrates dramatic circadian changes in DNA topology that modulates changes in the transcription rates.[21][22][29]

Visualizing the clockwork's "gears": structural biology of clock proteins

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Clock Protein KaiC hexamer, Synechococcus elongatus

The cyanobacterial circadian system is so far unique in that it is the only circadian system in which the structures of full-length clock proteins have been solved. In fact, the structures of all three of the Kai proteins have been determined. KaiC forms a hexamer that resembles a double doughnut with a central pore that is partially sealed at one end.[30] There are twelve ATP-binding sites in KaiC and the residues that are phosphorylated during the in vitro phosphorylation rhythm have been identified.[31][32] KaiA has two major domains and forms dimers in which the N-terminal domains are "swapped" with the C-terminal domains.[33][34] KaiB has been successfully crystallized from three different species of cyanobacteria and forms dimers or tetramers.[35][36]

The three-dimensional structures have been helpful in elucidating the cyanobacterial clock mechanism by providing concrete models for the ways in which the three Kai proteins interact and influence each other.[30][34][35][37][38][39][40]

 
KaiC Phosphorylation Cycle of the Cyanobacterial Clock

The structural approaches have also allowed the KaiA/KaiB/KaiC complexes to be visualized as a function of time, which enabled sophisticated mathematical modeling of the in vitro phosphorylation rhythm.[41] Therefore, the cyanobacterial clock components and their interactions can be visualized in four dimensions (three in space, one in time). The temporal formation patterns of the KaiA/KaiB/KaiC complex have been elucidated, along with an interpretation of the core mechanism based on the cycle of KaiC phosphorylation patterns and the dynamics of the KaiA/KaiB/KaiC complex.[42][43] (See the animation of the phsophorylation/complex cycle.) In addition, single-molecule methods (high-speed atomic force microscopy) have been applied to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on sub-second timescales.[44] These interactions regulate the circadian oscillation by modulating the magnesium binding in KaiC.[45]

While the KaiABC phosphorylation/complex cycle can explain key features of this biochemical circadian oscillator, especially how it can link to the output pathways that regulate global gene expression patterns,[46][19][20] it does not provide an explanation for why the oscillator has a period of approximately 24 hours, nor how it can be "temperature compensated." Phosphorylation/dephosphorylation reactions and protein complex associations/dissassociations can be very rapid, so why does this biochemical oscillator have a period that is as slow as 24 hours and yet still be so precise? One model is that the rate-limiting reaction that determines the period is the very slow rate of ATP hydrolysis by KaiC. KaiC hydrolyses ATP at the remarkably slow rate of only 15 ATP molecules per KaiC monomer per 24 hours. The rate of this ATPase activity is temperature compensated, and the activities of wild-type and period-mutant KaiC proteins are directly proportional to their in vivo circadian frequencies, suggesting that the ATPase activity defines the circadian period. Therefore, some authors have proposed that the KaiC ATPase activity constitutes the most fundamental reaction underlying circadian periodicity in cyanobacteria.[47] Structural analyses of the KaiC ATPase suggested that the slowness of this ATP hydrolysis arises from sequestration of a lytic water molecule in an unfavorable position and coupling of ATP hydrolysis to a peptide isomerization, thereby increasing the activation energy of ATP hydrolysis and slowing it to a 24 hour timescale.[48]

Circadian advantage

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Main article: Circadian advantage

In the context of bacterial circadian rhythms, specifically in cyanobacteria, circadian advantage refers to the improved competitive advantage of strains of cyanobacteria that "resonate" with the environmental circadian rhythm.[15] For example, consider a strain with a free-running period (FRP) of 24 hours that is co-cultured with a strain that has a free-running period (FRP) of 30 hours in a light-dark cycle of 12 hours light and 12 hours dark (LD 12:12). The strain that has a 24-hour FRP will out-compete the 30-hour strain over time under these LD 12:12 conditions. On the other hand, in a light-dark cycle of 15 hours light and 15 hours darkness, the 30-hour strain will out-compete the 24-hour strain.[15] Moreover, rhythmic strains of cyanobacteria will out-compete arhythmic strains in 24-h light/dark cycles, but in continuous light, arhythmic strains are able to co-exist with wild-type cells in mixed cultures.[14]

Other bacteria

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The only prokaryotic group with a well-documented circadian timekeeping mechanism is the cyanobacteria. Recent studies have suggested that there might be 24-hour timekeeping mechanisms among other prokaryotes.[43] The purple non-sulfur bacterium Rhodopseudomonas palustris is one such example, as it harbors homologs of KaiB and KaiC and exhibits adaptive KaiC-dependent growth enhancement in 24-hour cyclic environments.[49] However, R. palustris was reported to show a poor intrinsic free-running rhythm of nitrogen fixation under constant conditions. The lack of rhythm in R. palustris in constant conditions has implications for the adaptive value of intrinsic timekeeping mechanism.[43] Therefore, the R. palustris system was proposed as a "proto" circadian timekeeper that exhibit some parts of circadian systems (kaiB and kaiC homologs), but not all.[49]

There is some evidence of a circadian clock in Bacillus subtilis. Luciferase promoter assays showed gene expression patterns of ytvA, a gene encoding a blue light photoreceptor, that satisfied the criteria of a circadian clock. However, there has yet to be a robust demonstration of a clock in B. subtilis and the potential mechanisms of circadian gene regulation within B. subtilis remain unknown.[50]

Another interesting example is the case of the microbiome. It is possible that circadian clocks play a role in the gut microbiota behavior. These microorganisms experience daily changes because their hosts eat on a daily routine (consumption in the day for diurnal animals and in the night for nocturnal hosts). The presence of a daily timekeeper might allow gut bacteria to anticipate resources coming from the host temporally, thereby giving those species of bacteria a competitive advantage over other species in the gut. Some bacteria are known to take hints from the host circadian clock in the form of melatonin.[43] The disrupted gut microbiome has been proven to be related to a lot of diseases in humans gut microbiota. Thus, it is critical to our health to maintain a healthy gut microbiota. The host's circadian clock circadian rhythm controls the gut environment's ~24h cycle of many factors such as temperature changes, nutrients, certain hormones, bile acid levels, immune system functions.[51][52][43] The relative abundances of some gut bacteria, such as Firmicutes and Bacteroidetes, display a clear daily cycle.[53] In arrhythmic mice with clock-component dysfunctions, this rhythmicity disappears. Jet-lag and sleep deprivation can lead to the disruptions of the microbiome daily oscillations, but the changes are usually not dramatic.[54][55][56]

This interaction is bidirectional as the gut microbiota can also act on the hosts. For example, antibiotics can affect the rhythmic adherence of gut bacteria to the intestinal epithelium and in turn, rewire the hosts’ chromatin and transcription oscillations in the intestines and in the livers.[57]

 
Antibiotic treatment interferes with circadian rhythms in gut microbiome in clock gene mutated mice

Some of the current research in this field is focused on whether or not gut bacteria have intrinsic circadian rhythms. If so, researchers speculate that they may use their host's feeding patterns as zeitgebers. A long-term study on mice was conducted to determine whether the hosts’ rhythmic and arrhythmic feeding behaviors contributed differently to the recoveries of their gut microbiota from antibiotic treatment.[58] Researchers found that rhythmic behavior after antibiotic ablation facilitates complete recovery of the gut microbiota. On the other hand, arrhythmic behavior after antibiotic ablation hinders the gut microbiota's proper recovery. Instead, this behavior promotes microbiota recovery to a new steady status that is distinct from the original. The genus Turicibacter, proven to modulate the mood-related neurotransmitter serotonin,[59] was found to overly recover. This effect may lower the serotonin level in the gut, connecting the gut microbiome to effects on the host's mental health.

There are 4,616 bacterial species recognized in the human gut.[60] Only 2 of them, Klebsiella aerogenes and Bacillus subtilis, are currently reported to have circadian clocks.[50] [61] [62] It is suspected that other gut bacteria may have circadian clocks, too.

See also

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References

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  1. ^ a b c Ishiura M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, Tanabe A, Golden SS, Johnson CH, Kondo T (September 1998). "Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria". Science. 281 (5382): 1519–23. doi:10.1126/science.281.5382.1519. PMID 9727980.
  2. ^ Johnson CH, Golden SS, Ishiura M, Kondo T (July 1996). "Circadian clocks in prokaryotes". Molecular Microbiology. 21 (1): 5–11. doi:10.1046/j.1365-2958.1996.00613.x. PMID 8843429. S2CID 40431382.
  3. ^ Huang TC, Grobbelaar N (March 1995). "The circadian clock in the prokaryote Synechococcus RF-1". Microbiology. 141 (3): 535–540. doi:10.1099/13500872-141-3-535.
  4. ^ Lin RF, Huang TC (2009). "3. Circadian rhythm of Cyanothece RF-1 (Synechococcus RF-1)". In Ditty JL, Mackey SR, Johnson CH (eds.). Bacterial Circadian Programs. Springer. pp. 39–61. doi:10.1007/978-3-540-88431-6_3.
  5. ^ Sweeney BM, Borgese MB (1989). "A circadian rhythm in cell division in a prokaryote, the cyanobacterium Synechococcus WH7803". J. Phycol. 25: 183–6. doi:10.1111/j.0022-3646.1989.00183.x. S2CID 83576869.
  6. ^ a b Kondo T, Strayer CA, Kulkarni RD, Taylor W, Ishiura M, Golden SS, Johnson CH (June 1993). "Circadian rhythms in prokaryotes: luciferase as a reporter of circadian gene expression in cyanobacteria". Proceedings of the National Academy of Sciences of the United States of America. 90 (12): 5672–6. Bibcode:1993PNAS...90.5672K. doi:10.1073/pnas.90.12.5672. PMC 46783. PMID 8516317.
  7. ^ Johnson CH, Xu Y (2009). "4. The Decade of Discovery: How Synechococcus elongatus became a model circadian system 1990–2000". In Ditty JL, Mackey SR, Johnson CH (eds.). Bacterial Circadian Programs. Springer. pp. 63–86. doi:10.1007/978-3-540-88431-6_4.
  8. ^ Mihalcescu I, Hsing W, Leibler S (July 2004). "Resilient circadian oscillator revealed in individual cyanobacteria". Nature. 430 (6995): 81–5. Bibcode:2004Natur.430...81M. doi:10.1038/nature02533. PMID 15229601. S2CID 4390128.
  9. ^ Pittendrigh CS (1993). "Temporal organization: reflections of a Darwinian clock-watcher". Annual Review of Physiology. 55: 16–54. doi:10.1146/annurev.ph.55.030193.000313. PMID 8466172.
  10. ^ Mori T, Binder B, Johnson CH (September 1996). "Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours". Proceedings of the National Academy of Sciences of the United States of America. 93 (19): 10183–8. Bibcode:1996PNAS...9310183M. doi:10.1073/pnas.93.19.10183. PMC 38358. PMID 8816773.
  11. ^ Kondo T, Mori T, Lebedeva NV, Aoki S, Ishiura M, Golden SS (January 1997). "Circadian rhythms in rapidly dividing cyanobacteria". Science. 275 (5297): 224–7. doi:10.1126/science.275.5297.224. PMID 8985018. S2CID 31261881.
  12. ^ Mori T, Johnson CH (April 2001). "Independence of circadian timing from cell division in cyanobacteria". Journal of Bacteriology. 183 (8): 2439–44. doi:10.1128/JB.183.8.2439-2444.2001. PMC 95159. PMID 11274102.
  13. ^ Jabbur ML, Dani C, Spoelstra K, Dodd AN, Johnson CH (April 2024). "Evaluating the Adaptive Fitness of Circadian Clocks and their Evolution". J Biol Rhythms. 39 (2): 115–134. doi:10.1177/07487304231219206. PMC 10994774. PMID 38185853.
  14. ^ a b Woelfle MA, Ouyang Y, Phanvijhitsiri K, Johnson CH (August 2004). "The adaptive value of circadian clocks: an experimental assessment in cyanobacteria". Current Biology. 14 (16): 1481–6. doi:10.1016/j.cub.2004.08.023. PMID 15324665.
  15. ^ a b c Ouyang Y, Andersson CR, Kondo T, Golden SS, Johnson CH (July 1998). "Resonating circadian clocks enhance fitness in cyanobacteria". Proceedings of the National Academy of Sciences of the United States of America. 95 (15): 8660–4. Bibcode:1998PNAS...95.8660O. doi:10.1073/pnas.95.15.8660. PMC 21132. PMID 9671734.
  16. ^ Dodd AN, Salathia N, Hall A, Kévei E, Tóth R, Nagy F, Hibberd JM, Millar AJ, Webb AA (July 2005). "Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage". Science. 309 (5734): 630–3. doi:10.1126/science.1115581. PMID 16040710.
  17. ^ Spoelstra K, Wikelski M, Daan S, Loudon AS, Hau M (January 2016). "Natural selection against a circadian clock gene mutation in mice". Proc Natl Acad Sci U S A. 113 (3): 686–91. doi:10.1073/pnas.1516442113. PMC 4725470. PMID 26715747.
  18. ^ Liu Y, Tsinoremas NF, Johnson CH, Lebedeva NV, Golden SS, Ishiura M, Kondo T (June 1995). "Circadian orchestration of gene expression in cyanobacteria". Genes & Development. 9 (12): 1469–78. doi:10.1101/gad.9.12.1469. PMID 7601351.
  19. ^ a b c Markson JS, Piechura JR, Puszynska AM, O'Shea EK (December 2013). "Circadian control of global gene expression by the cyanobacterial master regulator RpaA". Cell. 155 (6): 1396–408. doi:10.1016/j.cell.2013.11.005. PMC 3935230. PMID 24315105.
  20. ^ a b c Chavan AG, Swan JA, Heisler J, Sancar C, Ernst DC, Fang M, Palacios JG, Spangler RK, Bagshaw CR, Tripathi S, Crosby P, Golden SS, Partch CL, LiWang A (October 2021). "Reconstitution of an intact clock reveals mechanisms of circadian timekeeping". Science. 374 (6564). doi:10.1126/science.abd4453. PMC 8686788. PMID 34618577.
  21. ^ a b Smith RM, Williams SB (May 2006). "Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus". Proceedings of the National Academy of Sciences of the United States of America. 103 (22): 8564–9. Bibcode:2006PNAS..103.8564S. doi:10.1073/pnas.0508696103. PMC 1482530. PMID 16707582.
  22. ^ a b Woelfle MA, Xu Y, Qin X, Johnson CH (November 2007). "Circadian rhythms of superhelical status of DNA in cyanobacteria". Proceedings of the National Academy of Sciences of the United States of America. 104 (47): 18819–24. Bibcode:2007PNAS..10418819W. doi:10.1073/pnas.0706069104. PMC 2141860. PMID 18000054.
  23. ^ Kondo T, Tsinoremas NF, Golden SS, Johnson CH, Kutsuna S, Ishiura M (November 1994). "Circadian clock mutants of cyanobacteria". Science. 266 (5188): 1233–6. Bibcode:1994Sci...266.1233K. doi:10.1126/science.7973706. PMID 7973706.
  24. ^ Dunlap JC, Loros JJ, DeCoursey PJ, eds. (2004). Chronobiology: Biological Timekeeping. Sunderland, MA.: Sinauer.
  25. ^ Xu Y, Mori T, Johnson CH (May 2003). "Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC". The EMBO Journal. 22 (9): 2117–26. doi:10.1093/emboj/cdg168. PMC 156062. PMID 12727878.
  26. ^ Nakahira Y, Katayama M, Miyashita H, Kutsuna S, Iwasaki H, Oyama T, Kondo T (January 2004). "Global gene repression by KaiC as a master process of prokaryotic circadian system". Proceedings of the National Academy of Sciences of the United States of America. 101 (3): 881–5. Bibcode:2004PNAS..101..881N. doi:10.1073/pnas.0307411100. PMC 321775. PMID 14709675.
  27. ^ Tomita J, Nakajima M, Kondo T, Iwasaki H (January 2005). "No transcription-translation feedback in circadian rhythm of KaiC phosphorylation". Science. 307 (5707): 251–4. Bibcode:2005Sci...307..251T. doi:10.1126/science.1102540. PMID 15550625. S2CID 9447128.
  28. ^ Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T (April 2005). "Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro". Science. 308 (5720): 414–5. Bibcode:2005Sci...308..414N. doi:10.1126/science.1108451. PMID 15831759. S2CID 24833877.
  29. ^ Vijayan V, Zuzow R, O'Shea EK (December 2009). "Oscillations in supercoiling drive circadian gene expression in cyanobacteria". Proceedings of the National Academy of Sciences of the United States of America. 106 (52): 22564–8. Bibcode:2009PNAS..10622564V. doi:10.1073/pnas.0912673106. PMC 2799730. PMID 20018699.
  30. ^ a b Pattanayek R, Wang J, Mori T, Xu Y, Johnson CH, Egli M (August 2004). "Visualizing a circadian clock protein: crystal structure of KaiC and functional insights". Molecular Cell. 15 (3): 375–88. doi:10.1016/j.molcel.2004.07.013. PMID 15304218.
  31. ^ Xu Y, Mori T, Pattanayek R, Pattanayek S, Egli M, Johnson CH (September 2004). "Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses". Proceedings of the National Academy of Sciences of the United States of America. 101 (38): 13933–8. doi:10.1073/pnas.0404768101. PMC 518856. PMID 15347809.
  32. ^ Nishiwaki T, Satomi Y, Nakajima M, Lee C, Kiyohara R, Kageyama H, Kitayama Y, Temamoto M, Yamaguchi A, Hijikata A, Go M, Iwasaki H, Takao T, Kondo T (September 2004). "Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942". Proceedings of the National Academy of Sciences of the United States of America. 101 (38): 13927–32. doi:10.1073/pnas.0403906101. PMC 518855. PMID 15347812.
  33. ^ Williams SB, Vakonakis I, Golden SS, LiWang AC (November 2002). "Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism". Proceedings of the National Academy of Sciences of the United States of America. 99 (24): 15357–62. Bibcode:2002PNAS...9915357W. doi:10.1073/pnas.232517099. PMC 137721. PMID 12438647.
  34. ^ a b Ye S, Vakonakis I, Ioerger TR, LiWang AC, Sacchettini JC (May 2004). "Crystal structure of circadian clock protein KaiA from Synechococcus elongatus". The Journal of Biological Chemistry. 279 (19): 20511–8. doi:10.1074/jbc.M400077200. PMID 15007067.
  35. ^ a b Garces RG, Wu N, Gillon W, Pai EF (April 2004). "Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC". The EMBO Journal. 23 (8): 1688–98. doi:10.1038/sj.emboj.7600190. PMC 394244. PMID 15071498.
  36. ^ Hitomi K, Oyama T, Han S, Arvai AS, Getzoff ED (May 2005). "Tetrameric architecture of the circadian clock protein KaiB. A novel interface for intermolecular interactions and its impact on the circadian rhythm". The Journal of Biological Chemistry. 280 (19): 19127–35. doi:10.1074/jbc.M411284200. PMID 15716274.
  37. ^ Vakonakis I, LiWang AC (July 2004). "Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation". Proceedings of the National Academy of Sciences of the United States of America. 101 (30): 10925–30. Bibcode:2004PNAS..10110925V. doi:10.1073/pnas.0403037101. PMC 503721. PMID 15256595.
  38. ^ Pattanayek R, Williams DR, Pattanayek S, Xu Y, Mori T, Johnson CH, Stewart PL, Egli M (May 2006). "Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods". The EMBO Journal. 25 (9): 2017–28. doi:10.1038/sj.emboj.7601086. PMC 1456936. PMID 16628225.
  39. ^ Kim YI, Dong G, Carruthers CW, Golden SS, LiWang A (September 2008). "The day/night switch in KaiC, a central oscillator component of the circadian clock of cyanobacteria". Proceedings of the National Academy of Sciences of the United States of America. 105 (35): 12825–30. Bibcode:2008PNAS..10512825K. doi:10.1073/pnas.0800526105. PMC 2529086. PMID 18728181.
  40. ^ Pattanayek R, Williams DR, Pattanayek S, Mori T, Johnson CH, Stewart PL, Egli M (June 2008). "Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation". The EMBO Journal. 27 (12): 1767–78. doi:10.1038/emboj.2008.104. PMC 2435126. PMID 18497745.
  41. ^ Mori T, Williams DR, Byrne MO, Qin X, Egli M, Mchaourab HS, Stewart PL, Johnson CH (April 2007). "Elucidating the ticking of an in vitro circadian clockwork". PLOS Biology. 5 (4): e93. doi:10.1371/journal.pbio.0050093. PMC 1831719. PMID 17388688.
  42. ^ Swan JA, Golden SS, LiWang A, Partch CL (April 2018). "Structure, function, and mechanism of the core circadian clock in cyanobacteria". The Journal of Biological Chemistry. 293 (14): 5026–34. doi:10.1074/jbc.TM117.001433. PMC 5892564. PMID 29440392.
  43. ^ a b c d e Johnson CH, Zhao C, Xu Y, Mori T (April 2017). "Timing the day: what makes bacterial clocks tick?". Nature Reviews. Microbiology. 15 (4): 232–242. doi:10.1038/nrmicro.2016.196. PMC 5696799. PMID 28216658.
  44. ^ Mori T, Sugiyama S, Byrne M, Johnson CH, Uchihashi T, Ando T (August 2018). "Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time". Nature Communications. 9 (1): 3245. Bibcode:2018NatCo...9.3245M. doi:10.1038/s41467-018-05438-4. PMC 6092398. PMID 30108211.
  45. ^ Jeong, Young M.; Dias, Cristiano; Diekman, Casey; Brochon, Helene; Kim, Pyonghwa; Kaur, Manpreet; Kim, Yong-Sung; Jang, Hye-In; Kim, Yong-Ick (August 2019). "Magnesium Regulates the Circadian Oscillator in Cyanobacteria". Journal of Biological Rhythms. 34 (4): 380–390. doi:10.1177/0748730419851655. ISSN 0748-7304. PMID 31216910. S2CID 107565874.
  46. ^ Qin X, Byrne M, Xu Y, Mori T, Johnson CH. "Coupling of a core post-translational pacemaker to a slave transcription/translation feedback loop in a circadian system". PLoS Biology. 8 (e1000394). doi:10.1371/journal.pbio.1000394. PMC 2885980. PMID 20563306.
  47. ^ Terauchi K, Kitayama Y, Nishiwaki T, Miwa K, Murayama Y, Oyama T, Kondo T (October 2007). "ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria". Proc Natl Acad Sci U S A. 104 (41): 16377–81. doi:10.1073/pnas.0706292104. PMC 2042214.
  48. ^ Abe J, Hiyama TB, Mukaiyama A, Son S, Mori T, Saito S, Osako M, Wolanin J, Yamashita E, Kondo T, Akiyama S (July 2015). "Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock". Science. 349 (6245): 312–6. doi:10.1126/science.1261040. PMID 26113637.
  49. ^ a b Ma P, Mori T, Zhao C, Thiel T, Johnson CH (March 2016). "Evolution of KaiC-Dependent Timekeepers: A Proto-circadian Timing Mechanism Confers Adaptive Fitness in the Purple Bacterium Rhodopseudomonas palustris". PLOS Genetics. 12 (3): e1005922. doi:10.1371/journal.pgen.1005922. PMC 4794148. PMID 26982486.
  50. ^ a b Eelderink-Chen, Zheng; Bosman, Jasper; Sartor, Francesca; Dodd, Antony N.; Kovács, Ákos T.; Merrow, Martha (2021). "A circadian clock in a nonphotosynthetic prokaryote". Science Advances. 7 (2): eabe2086. Bibcode:2021SciA....7.2086E. doi:10.1126/sciadv.abe2086. PMC 7793578. PMID 33523996.
  51. ^ Liang X, FitzGerald GA (December 2017). "Timing the Microbes: The Circadian Rhythm of the Gut Microbiome". J Biol Rhythms. 32 (6): 505–515. doi:10.1177/0748730417729066. PMID 28862076.
  52. ^ Ma K, Xiao R, Tseng HT, Shan L, Fu L, Moore DD (August 2009). "Circadian dysregulation disrupts bile acid homeostasis". PLoS One. 4 (8): e6843. doi:10.1371/journal.pone.0006843. PMC 2730029. PMID 19718444.
  53. ^ Pickel L, Lee JH, Maughan H, Shi IQ, Verma N, Yeung C, Guttman D, Sung HK (July 2022). "Circadian rhythms in metabolic organs and the microbiota during acute fasting in mice". Physiol Rep. 10 (14): e15393. doi:10.14814/phy2.15393. PMC 9295129. PMID 35851583.
  54. ^ Liang X, Bushman FD, FitzGerald GA (August 2015). "Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock". Proc Natl Acad Sci U S A. 112 (33): 10479–84. doi:10.1073/pnas.1501305112. PMC 4547234. PMID 26240359.
  55. ^ Thaiss CA, Zeevi D, Levy M, Zilberman-Schapira G, Suez J, Tengeler AC, Abramson L, Katz MN, Korem T, Zmora N, Kuperman Y, Biton I, Gilad S, Harmelin A, Shapiro H, Halpern Z, Segal E, Elinav E (October 2014). "Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis". Cell. 159 (3): 514–29. doi:10.1016/j.cell.2014.09.048. PMID 25417104.
  56. ^ Zhang SL, Bai L, Goel N, Bailey A, Jang CJ, Bushman FD, Meerlo P, Dinges DF, Sehgal A (February 2017). "Human and rat gut microbiome composition is maintained following sleep restriction". Proc Natl Acad Sci U S A. 114 (8): E1564–E1571. doi:10.1073/pnas.1620673114. PMC 5338418. PMID 28179566.
  57. ^ Thaiss CA, Levy M, Korem T, Dohnalová L, Shapiro H, Jaitin DA, David E, Winter DR, Gury-BenAri M, Tatirovsky E, Tuganbaev T, Federici S, Zmora N, Zeevi D, Dori-Bachash M, Pevsner-Fischer M, Kartvelishvily E, Brandis A, Harmelin A, Shibolet O, Halpern Z, Honda K, Amit I, Segal E, Elinav E (December 2016). "Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations". Cell. 167 (6): 1495–1510. doi:10.1016/j.cell.2016.11.003. PMID 27912059.
  58. ^ Zhao C, Kelly K, Jabbur ML, Paguaga M, Behringer M, Johnson CH (November 2022). "Host circadian behaviors exert only weak selective pressure on the gut microbiome under stable conditions but are critical for recovery from antibiotic treatment". PLoS Biol. 20 (11): e3001865. doi:10.1371/journal.pbio.3001865. PMC 9645659. PMID 36350921.
  59. ^ Fung TC, Vuong HE, Luna CD, Pronovost GN, Aleksandrova AA, Riley NG, Vavilina A, McGinn J, Rendon T, Forrest LR, Hsiao EY (December 2019). "Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut". Nat Microbiol. 4 (12): 2064–73. doi:10.1038/s41564-019-0540-4. PMC 6879823. PMID 31477894.
  60. ^ Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD (January 2021). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nat Biotechnol. 39 (1): 105–114. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
  61. ^ Paulose JK, Cassone CV, Graniczkowska KB, Cassone VM (September 2019). "Entrainment of the Circadian Clock of the Enteric Bacterium Klebsiella aerogenes by Temperature Cycles". iScience. 19: 1202–13. doi:10.1016/j.isci.2019.09.007. PMC 6831877. PMID 31551197.
  62. ^ Paulose JK, Wright JM, Patel AG, Cassone VM (2016). "Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity". PLoS One. 11 (1): e0146643. doi:10.1371/journal.pone.0146643. PMC 4709092. PMID 26751389.

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