1
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Zamudio-Beltrán LE, Bossu CM, Bueno-Hernández AA, Dunn PO, Sly ND, Rayne C, Anderson EC, Hernández-Baños BE, Ruegg KC. Parallel and convergent evolution in genes underlying seasonal migration. Evol Lett 2025; 9:189-208. [PMID: 40191407 PMCID: PMC11968193 DOI: 10.1093/evlett/qrae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/05/2024] [Accepted: 11/11/2024] [Indexed: 04/09/2025] Open
Abstract
Seasonal migration has fascinated scientists and natural historians for centuries. While the genetic basis of migration has been widely studied across different taxa, there is little consensus regarding which genomic regions play a role in the ability to migrate and whether they are similar across species. Here, we examine the genetic basis of intraspecific variation within and between distinct migratory phenotypes in a songbird. We focus on the Common Yellowthroat (Geothlypis trichas) as a model system because the polyphyletic origin of eastern and western clades across North America provides a strong framework for understanding the extent to which there has been parallel or convergent evolution in the genes associated with migratory behavior. First, we investigate genome-wide population genetic structure in the Common Yellowthroat in 196 individuals collected from 22 locations across breeding range. Then, to identify candidate genes involved in seasonal migration, we identify signals of putative selection in replicate comparisons between resident and migratory phenotypes within and between eastern and western clades. Overall, we find wide-spread support for parallel evolution at the genic level, particularly in genes that mediate biological timekeeping. However, we find little evidence of parallelism at the individual SNP level, supporting the idea that there are multiple genetic pathways involved in the modulation of migration.
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Affiliation(s)
- Luz E Zamudio-Beltrán
- Facultad de Estudios Superiores Zaragoza, UNAM, Mexico City, Mexico
- Facultad de Ciencias, UNAM, Mexico City, Mexico
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | | | - Peter O Dunn
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Nicholas D Sly
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Christine Rayne
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Eric C Anderson
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | | | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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2
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Davidson K, Pickering AM. The proteasome: A key modulator of nervous system function, brain aging, and neurodegenerative disease. Front Cell Dev Biol 2023; 11:1124907. [PMID: 37123415 PMCID: PMC10133520 DOI: 10.3389/fcell.2023.1124907] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
The proteasome is a large multi-subunit protease responsible for the degradation and removal of oxidized, misfolded, and polyubiquitinated proteins. The proteasome plays critical roles in nervous system processes. This includes maintenance of cellular homeostasis in neurons. It also includes roles in long-term potentiation via modulation of CREB signaling. The proteasome also possesses roles in promoting dendritic spine growth driven by proteasome localization to the dendritic spines in an NMDA/CaMKIIα dependent manner. Proteasome inhibition experiments in varied organisms has been shown to impact memory, consolidation, recollection and extinction. The proteasome has been further shown to impact circadian rhythm through modulation of a range of 'clock' genes, and glial function. Proteasome function is impaired as a consequence both of aging and neurodegenerative diseases. Many studies have demonstrated an impairment in 26S proteasome function in the brain and other tissues as a consequence of age, driven by a disassembly of 26S proteasome in favor of 20S proteasome. Some studies also show proteasome augmentation to correct age-related deficits. In amyotrophic lateral sclerosis Alzheimer's, Parkinson's and Huntington's disease proteasome function is impaired through distinct mechanisms with impacts on disease susceptibility and progression. Age and neurodegenerative-related deficits in the function of the constitutive proteasome are often also accompanied by an increase in an alternative form of proteasome called the immunoproteasome. This article discusses the critical role of the proteasome in the nervous system. We then describe how proteasome dysfunction contributes to brain aging and neurodegenerative disease.
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Affiliation(s)
- Kanisa Davidson
- Department of Psychology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Andrew M. Pickering
- Center for Neurodegeneration and Experimental Therapeutics (CNET), Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
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3
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Tabuloc CA, Cai YD, Kwok RS, Chan EC, Hidalgo S, Chiu JC. CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters. PLoS Genet 2023; 19:e1010649. [PMID: 36809369 PMCID: PMC9983840 DOI: 10.1371/journal.pgen.1010649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/03/2023] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Circadian clock and chromatin-remodeling complexes are tightly intertwined systems that regulate rhythmic gene expression. The circadian clock promotes rhythmic expression, timely recruitment, and/or activation of chromatin remodelers, while chromatin remodelers regulate accessibility of clock transcription factors to the DNA to influence expression of clock genes. We previously reported that the BRAHMA (BRM) chromatin-remodeling complex promotes the repression of circadian gene expression in Drosophila. In this study, we investigated the mechanisms by which the circadian clock feeds back to modulate daily BRM activity. Using chromatin immunoprecipitation, we observed rhythmic BRM binding to clock gene promoters despite constitutive BRM protein expression, suggesting that factors other than protein abundance are responsible for rhythmic BRM occupancy at clock-controlled loci. Since we previously reported that BRM interacts with two key clock proteins, CLOCK (CLK) and TIMELESS (TIM), we examined their effect on BRM occupancy to the period (per) promoter. We observed reduced BRM binding to the DNA in clk null flies, suggesting that CLK is involved in enhancing BRM occupancy to initiate transcriptional repression at the conclusion of the activation phase. Additionally, we observed reduced BRM binding to the per promoter in flies overexpressing TIM, suggesting that TIM promotes BRM removal from DNA. These conclusions are further supported by elevated BRM binding to the per promoter in flies subjected to constant light and experiments in Drosophila tissue culture in which the levels of CLK and TIM are manipulated. In summary, this study provides new insights into the reciprocal regulation between the circadian clock and the BRM chromatin-remodeling complex.
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Affiliation(s)
- Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Rosanna S. Kwok
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Elizabeth C. Chan
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
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4
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Abdalla OHMH, Mascarenhas B, Cheng HYM. Death of a Protein: The Role of E3 Ubiquitin Ligases in Circadian Rhythms of Mice and Flies. Int J Mol Sci 2022; 23:ijms231810569. [PMID: 36142478 PMCID: PMC9502492 DOI: 10.3390/ijms231810569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/04/2022] Open
Abstract
Circadian clocks evolved to enable organisms to anticipate and prepare for periodic environmental changes driven by the day–night cycle. This internal timekeeping mechanism is built on autoregulatory transcription–translation feedback loops that control the rhythmic expression of core clock genes and their protein products. The levels of clock proteins rise and ebb throughout a 24-h period through their rhythmic synthesis and destruction. In the ubiquitin–proteasome system, the process of polyubiquitination, or the covalent attachment of a ubiquitin chain, marks a protein for degradation by the 26S proteasome. The process is regulated by E3 ubiquitin ligases, which recognize specific substrates for ubiquitination. In this review, we summarize the roles that known E3 ubiquitin ligases play in the circadian clocks of two popular model organisms: mice and fruit flies. We also discuss emerging evidence that implicates the N-degron pathway, an alternative proteolytic system, in the regulation of circadian rhythms. We conclude the review with our perspectives on the potential for the proteolytic and non-proteolytic functions of E3 ubiquitin ligases within the circadian clock system.
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Affiliation(s)
- Osama Hasan Mustafa Hasan Abdalla
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Brittany Mascarenhas
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
- Correspondence:
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5
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Ukita Y, Okumura M, Chihara T. Ubiquitin proteasome system in circadian rhythm and sleep homeostasis: Lessons from Drosophila. Genes Cells 2022; 27:381-391. [PMID: 35438236 PMCID: PMC9322287 DOI: 10.1111/gtc.12935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/30/2022]
Abstract
Sleep is regulated by two main processes: the circadian clock and sleep homeostasis. Circadian rhythms have been well studied at the molecular level. In the Drosophila circadian clock neurons, the core clock proteins are precisely regulated by post-translational modifications and degraded via the ubiquitin-proteasome system (UPS). Sleep homeostasis, however, is less understood; nevertheless, recent reports suggest that proteasome-mediated degradation of core clock proteins or synaptic proteins contributes to the regulation of sleep amount. Here, we review the molecular mechanism of the UPS and summarize the role of protein degradation in the regulation of circadian clock and homeostatic sleep in Drosophila. Moreover, we discuss the potential interaction between circadian clock and homeostatic sleep regulation with a prime focus on E3 ubiquitin ligases.
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Affiliation(s)
- Yumiko Ukita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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6
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Lamaze A, Chen C, Leleux S, Xu M, George R, Stanewsky R. A natural timeless polymorphism allowing circadian clock synchronization in "white nights". Nat Commun 2022; 13:1724. [PMID: 35361756 PMCID: PMC8971440 DOI: 10.1038/s41467-022-29293-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Abstract
Daily temporal organisation offers a fitness advantage and is determined by an interplay between environmental rhythms and circadian clocks. While light:dark cycles robustly synchronise circadian clocks, it is not clear how animals experiencing only weak environmental cues deal with this problem. Like humans, Drosophila originate in sub-Saharan Africa and spread North up to the polar circle, experiencing long summer days or even constant light (LL). LL disrupts clock function, due to constant activation of CRYPTOCHROME, which induces degradation of the clock protein TIMELESS (TIM), but temperature cycles are able to overcome these deleterious effects of LL. We show here that for this to occur a recently evolved natural timeless allele (ls-tim) is required, encoding the less light-sensitive L-TIM in addition to S-TIM, the only form encoded by the ancient s-tim allele. We show that only ls-tim flies can synchronise their behaviour to semi-natural conditions typical for Northern European summers, suggesting that this functional gain is driving the Northward ls-tim spread. The genus Drosophila originate in subSaharan Africa and spread North up to the polar circle where they experience long days in the summer or even constant light. Here, the authors show that a form of the TIMELESS protein enables flies to synchronise their behavioural activity to long summer days
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Affiliation(s)
- Angelique Lamaze
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany.
| | - Chenghao Chen
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.
| | - Solene Leleux
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Min Xu
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Rebekah George
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany.
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7
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Lamaze A, Chen C, Leleux S, Xu M, George R, Stanewsky R. A natural timeless polymorphism allowing circadian clock synchronization in "white nights". Nat Commun 2022; 13:1724. [PMID: 35361756 PMCID: PMC8971440 DOI: 10.1038/s41467-022-29293-6|] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/08/2022] [Indexed: 06/19/2023] Open
Abstract
Daily temporal organisation offers a fitness advantage and is determined by an interplay between environmental rhythms and circadian clocks. While light:dark cycles robustly synchronise circadian clocks, it is not clear how animals experiencing only weak environmental cues deal with this problem. Like humans, Drosophila originate in sub-Saharan Africa and spread North up to the polar circle, experiencing long summer days or even constant light (LL). LL disrupts clock function, due to constant activation of CRYPTOCHROME, which induces degradation of the clock protein TIMELESS (TIM), but temperature cycles are able to overcome these deleterious effects of LL. We show here that for this to occur a recently evolved natural timeless allele (ls-tim) is required, encoding the less light-sensitive L-TIM in addition to S-TIM, the only form encoded by the ancient s-tim allele. We show that only ls-tim flies can synchronise their behaviour to semi-natural conditions typical for Northern European summers, suggesting that this functional gain is driving the Northward ls-tim spread.
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Affiliation(s)
- Angelique Lamaze
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany.
| | - Chenghao Chen
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.
| | - Solene Leleux
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Min Xu
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Rebekah George
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany.
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8
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Salim S, Banu A, Alwa A, Gowda SBM, Mohammad F. The gut-microbiota-brain axis in autism: what Drosophila models can offer? J Neurodev Disord 2021; 13:37. [PMID: 34525941 PMCID: PMC8442445 DOI: 10.1186/s11689-021-09378-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/06/2021] [Indexed: 12/28/2022] Open
Abstract
The idea that alterations in gut-microbiome-brain axis (GUMBA)-mediated communication play a crucial role in human brain disorders like autism remains a topic of intensive research in various labs. Gastrointestinal issues are a common comorbidity in patients with autism spectrum disorder (ASD). Although gut microbiome and microbial metabolites have been implicated in the etiology of ASD, the underlying molecular mechanism remains largely unknown. In this review, we have summarized recent findings in human and animal models highlighting the role of the gut-brain axis in ASD. We have discussed genetic and neurobehavioral characteristics of Drosophila as an animal model to study the role of GUMBA in ASD. The utility of Drosophila fruit flies as an amenable genetic tool, combined with axenic and gnotobiotic approaches, and availability of transgenic flies may reveal mechanistic insight into gut-microbiota-brain interactions and the impact of its alteration on behaviors relevant to neurological disorders like ASD.
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Affiliation(s)
- Safa Salim
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Ayesha Banu
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Amira Alwa
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Swetha B M Gowda
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Farhan Mohammad
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar.
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9
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Rivas GBS, Zhou J, Merlin C, Hardin PE. CLOCKWORK ORANGE promotes CLOCK-CYCLE activation via the putative Drosophila ortholog of CLOCK INTERACTING PROTEIN CIRCADIAN. Curr Biol 2021; 31:4207-4218.e4. [PMID: 34331859 DOI: 10.1016/j.cub.2021.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/04/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
The Drosophila circadian clock is driven by a transcriptional feedback loop in which CLOCK-CYCLE (CLK-CYC) binds E-boxes to transcribe genes encoding the PERIOD-TIMELESS (PER-TIM) repressor, which releases CLK-CYC from E-boxes to inhibit transcription. CLOCKWORK ORANGE (CWO) reinforces PER-TIM repression by binding E-boxes to maintain PER-TIM bound CLK-CYC off DNA, but also promotes CLK-CYC transcription through an unknown mechanism. To determine how CWO activates CLK-CYC transcription, we identified CWO target genes that are upregulated in the absence of CWO repression, conserved in mammals, and preferentially expressed in brain pacemaker neurons. Among the genes identified was a putative ortholog of mouse Clock Interacting Protein Circadian (Cipc), which represses CLOCK-BMAL1 transcription. Reducing or eliminating Drosophila Cipc expression shortens period, while overexpressing Cipc lengthens period, which is consistent with previous work showing that Drosophila Cipc represses CLK-CYC transcription in S2 cells. Cipc represses CLK-CYC transcription in vivo, but not uniformly, as per is strongly repressed, tim less so, and vri hardly at all. Long period rhythms in cwo mutant flies are largely rescued when Cipc expression is reduced or eliminated, indicating that increased Cipc expression mediates the period lengthening of cwo mutants. Consistent with this behavioral rescue, eliminating Cipc rescues the decreased CLK-CYC transcription in cwo mutant flies, where per is strongly rescued, tim is moderately rescued, and vri shows little rescue. These results suggest a mechanism for CWO-dependent CLK-CYC activation: CWO inhibition of CIPC repression promotes CLK-CYC transcription. This mechanism may be conserved since cwo and Cipc perform analogous roles in the mammalian circadian clock.
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Affiliation(s)
- Gustavo B S Rivas
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Jian Zhou
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Christine Merlin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Paul E Hardin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA.
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10
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Kula-Eversole E, Lee DH, Samba I, Yildirim E, Levine DC, Hong HK, Lear BC, Bass J, Rosbash M, Allada R. Phosphatase of Regenerating Liver-1 Selectively Times Circadian Behavior in Darkness via Function in PDF Neurons and Dephosphorylation of TIMELESS. Curr Biol 2021; 31:138-149.e5. [PMID: 33157022 PMCID: PMC7855481 DOI: 10.1016/j.cub.2020.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/25/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022]
Abstract
The timing of behavior under natural light-dark conditions is a function of circadian clocks and photic input pathways, but a mechanistic understanding of how these pathways collaborate in animals is lacking. Here we demonstrate in Drosophila that the Phosphatase of Regenerating Liver-1 (PRL-1) sets period length and behavioral phase gated by photic signals. PRL-1 knockdown in PDF clock neurons dramatically lengthens circadian period. PRL-1 mutants exhibit allele-specific interactions with the light- and clock-regulated gene timeless (tim). Moreover, we show that PRL-1 promotes TIM accumulation and dephosphorylation. Interestingly, the PRL-1 mutant period lengthening is suppressed in constant light, and PRL-1 mutants display a delayed phase under short, but not long, photoperiod conditions. Thus, our studies reveal that PRL-1-dependent dephosphorylation of TIM is a core mechanism of the clock that sets period length and phase in darkness, enabling the behavioral adjustment to change day-night cycles.
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Affiliation(s)
| | - Da Hyun Lee
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Ima Samba
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Evrim Yildirim
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Daniel C Levine
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hee-Kyung Hong
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bridget C Lear
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Joseph Bass
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, MA 02445, USA
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.
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11
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Srikanta SB, Cermakian N. To Ub or not to Ub: Regulation of circadian clocks by ubiquitination and deubiquitination. J Neurochem 2020; 157:11-30. [PMID: 32717140 DOI: 10.1111/jnc.15132] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/28/2022]
Abstract
Circadian clocks are internal timing systems that enable organisms to adjust their behavioral and physiological rhythms to the daily changes of their environment. These clocks generate self-sustained oscillations at the cellular, tissue, and behavioral level. The rhythm-generating mechanism is based on a gene expression network with a delayed negative feedback loop that causes the transcripts to oscillate with a period of approximately 24 hr. This oscillatory nature of the proteins involved in this network necessitates that they are intrinsically unstable, with a short half-life. Hence, post-translational modifications (PTMs) are important to precisely time the presence, absence, and interactions of these proteins at appropriate times of the day. Ubiquitination and deubiquitination are counter-balancing PTMs which play a key role in this regulatory process. In this review, we take a comprehensive look at the roles played by the processes of ubiquitination and deubiquitination in the clock machinery of the most commonly studied eukaryotic models of the circadian clock: plants, fungi, fruit flies, and mammals. We present the effects exerted by ubiquitinating and deubiquitinating enzymes on the stability, but also the activity, localization, and interactions of clock proteins. Overall, these PTMs have key roles in regulating not only the pace of the circadian clocks but also their response to external cues and their control of cellular functions.
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Affiliation(s)
- Shashank Bangalore Srikanta
- Integrated Program in Neuroscience, McGill University, Montréal, QC, Canada.,Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada
| | - Nicolas Cermakian
- Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada.,Department of Psychiatry, McGill University, Montréal, QC, Canada
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12
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Sharma A, Lee S, Kim H, Yoon H, Ha S, Kang SU. Molecular Crosstalk Between Circadian Rhythmicity and the Development of Neurodegenerative Disorders. Front Neurosci 2020; 14:844. [PMID: 32848588 PMCID: PMC7424028 DOI: 10.3389/fnins.2020.00844] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
Neurodegenerative disorders have been shown to exhibit substantial interconnectedness with circadian rhythmicity. Alzheimer's patients exhibit high degradation of the suprachiasmatic nucleus (SCN), the central endogenous circadian timekeeper, and Parkinson's patients have highly disrupted peripheral clock gene expression. Disrupted sleep patterns are highly evident in patients with neurodegenerative diseases; fragmented sleep has been shown to affect tau-protein accumulation in Alzheimer's patients, and rapid eye movement (REM) behavioral disorder is observed in a significant amount of Parkinson's patients. Although numerous studies exist analyzing the mechanisms of neurodegeneration and circadian rhythm function independently, molecular mechanisms establishing specific links between the two must be explored further. Thus, in this review, we explore the possible intersecting molecular mechanisms between circadian rhythm and neurodegeneration, with a particular focus on Parkinson's disease. We provide evidence for potential influences of E3 ligase and poly adenosine diphosphate (ADP-ribose) polymerase 1 (PARP1) activity on neurodegenerative pathology. The cellular stress and subsequent DNA damage signaling imposed by hyperactivity of these multiple molecular systems in addition to aberrant circadian rhythmicity lead to extensive protein aggregation such as α-synuclein pre-formed fibrils (α-Syn PFFs), suggesting a specific molecular pathway linking circadian rhythmicity, PARP1/E3 ligase activity, and Parkinson's disease.
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Affiliation(s)
- Arastu Sharma
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sehyun Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hoonseo Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hargsoon Yoon
- Neural Engineering and Nano Electronics Laboratory, Department of Engineering, Norfolk State University, Norfolk, VA, United States
| | - Shinwon Ha
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sung Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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13
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Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle. Cell Rep 2019; 23:2273-2282. [PMID: 29791839 DOI: 10.1016/j.celrep.2018.04.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/10/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022] Open
Abstract
Circadian clocks have evolved as time-measuring molecular devices to help organisms adapt their physiology to daily changes in light and temperature. Transcriptional oscillations account for a large fraction of rhythmic protein abundance. However, cycling of various posttranslational modifications, such as ubiquitylation, also contributes to shape the rhythmic protein landscape. In this study, we used an in vivo ubiquitin labeling assay to investigate the circadian ubiquitylated proteome of Drosophila melanogaster. We find that cyclic ubiquitylation affects MEGATOR (MTOR), a chromatin-associated nucleoporin that, in turn, feeds back to regulate the core molecular oscillator. Furthermore, we show that the ubiquitin ligase subunits CULLIN-3 (CUL-3) and SUPERNUMERARY LIMBS (SLMB) cooperate for ubiquitylating the TIMELESS protein. These findings stress the importance of ubiquitylation pathways in the Drosophila circadian clock and reveal a key component of this system.
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14
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Lee C. CRY arrests Cop1 to regulate circadian rhythms in mammals. Cell Div 2019; 14:12. [PMID: 31700528 PMCID: PMC6825355 DOI: 10.1186/s13008-019-0055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022] Open
Abstract
Cryptochromes (CRYs) are UVA and blue light photoreceptors present in all major evolutionary lineages ranging from cyanobacteria to plants and animals, including mammals. In plants, blue light activates CRYs to induce photomorphogenesis by inhibiting the CRL4Cop1 E3 ligase complex which regulates the degradation of critical transcription factors involved in plant development and growth. However, in mammals, CRYs do not physically interact with Cop1, and of course mammals are not photomorphogenic, leading to the belief that the CRY-Cop1 axis is not conserved in mammals. This belief was recently overturned by Rizzini et al., who showed that although mammalian CRYs do not inhibit Cop1 activity in a light-dependent manner, they antagonize Cop1 activity by displacing Cop1 from CRL4 E3 ligase complex. Because CRYs oscillate, they act in a circadian manner resulting in daily oscillations in Cop1 substrates and the downstream pathways that they regulate. The conserved antagonism of Cop1 by CRY indicates that the CRY-Cop1 axis has an ancient origin, and was repurposed by evolution to regulate photomorphogenesis in plants and circadian rhythms in mammals.
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Affiliation(s)
- Choogon Lee
- Department of Biomedical Sciences, Program in Neuroscience, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306 USA
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15
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Kim JK. Protein sequestration versus Hill-type repression in circadian clock models. IET Syst Biol 2018; 10:125-35. [PMID: 27444022 DOI: 10.1049/iet-syb.2015.0090] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Circadian (∼24 h) clocks are self-sustained endogenous oscillators with which organisms keep track of daily and seasonal time. Circadian clocks frequently rely on interlocked transcriptional-translational feedback loops to generate rhythms that are robust against intrinsic and extrinsic perturbations. To investigate the dynamics and mechanisms of the intracellular feedback loops in circadian clocks, a number of mathematical models have been developed. The majority of the models use Hill functions to describe transcriptional repression in a way that is similar to the Goodwin model. Recently, a new class of models with protein sequestration-based repression has been introduced. Here, the author discusses how this new class of models differs dramatically from those based on Hill-type repression in several fundamental aspects: conditions for rhythm generation, robust network designs and the periods of coupled oscillators. Consistently, these fundamental properties of circadian clocks also differ among Neurospora, Drosophila, and mammals depending on their key transcriptional repression mechanisms (Hill-type repression or protein sequestration). Based on both theoretical and experimental studies, this review highlights the importance of careful modelling of transcriptional repression mechanisms in molecular circadian clocks.
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Affiliation(s)
- Jae Kyoung Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro Yuseong-gu, Daejeon, 34141, Korea.
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16
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Mendoza-Viveros L, Bouchard-Cannon P, Hegazi S, Cheng AH, Pastore S, Cheng HYM. Molecular modulators of the circadian clock: lessons from flies and mice. Cell Mol Life Sci 2017; 74:1035-1059. [PMID: 27689221 PMCID: PMC11107503 DOI: 10.1007/s00018-016-2378-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/03/2016] [Accepted: 09/22/2016] [Indexed: 12/16/2022]
Abstract
Circadian timekeeping is a ubiquitous mechanism that enables organisms to maintain temporal coordination between internal biological processes and time of the local environment. The molecular basis of circadian rhythms lies in a set of transcription-translation feedback loops (TTFLs) that drives the rhythmic transcription of core clock genes, whose level and phase of expression serve as the marker of circadian time. However, it has become increasingly evident that additional regulatory mechanisms impinge upon the TTFLs to govern the properties and behavior of the circadian clock. Such mechanisms include changes in chromatin architecture, interactions with other transcription factor networks, post-transcriptional control by RNA modifications, alternative splicing and microRNAs, and post-translational regulation of subcellular trafficking and protein degradation. In this review, we will summarize the current knowledge of circadian clock regulation-from transcriptional to post-translational-drawing from literature pertaining to the Drosophila and murine circadian systems.
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Affiliation(s)
- Lucia Mendoza-Viveros
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Pascale Bouchard-Cannon
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Sara Hegazi
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Stephen Pastore
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada.
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada.
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17
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Kwok RS, Lam VH, Chiu JC. Understanding the role of chromatin remodeling in the regulation of circadian transcription in Drosophila. Fly (Austin) 2016; 9:145-54. [PMID: 26926115 PMCID: PMC4862430 DOI: 10.1080/19336934.2016.1143993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circadian clocks enable organisms to anticipate daily changes in the environment and coordinate temporal rhythms in physiology and behavior with the 24-h day-night cycle. The robust cycling of circadian gene expression is critical for proper timekeeping, and is regulated by transcription factor binding, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Recently, it has become clear that dynamic alterations in chromatin landscape at the level of histone posttranslational modification and nucleosome density facilitate rhythms in transcription factor recruitment and RNAPII activity, and are essential for progression through activating and repressive phases of circadian transcription. Here, we discuss the characterization of the BRAHMA (BRM) chromatin-remodeling protein in Drosophila in the context of circadian clock regulation. By dissecting its catalytic vs. non-catalytic activities, we propose a model in which the non-catalytic activity of BRM functions to recruit repressive factors to limit the transcriptional output of CLOCK (CLK) during the active phase of circadian transcription, while the primary function of the ATP-dependent catalytic activity is to tune and prevent over-recruitment of negative regulators by increasing nucleosome density. Finally, we divulge ongoing efforts and investigative directions toward a deeper mechanistic understanding of transcriptional regulation of circadian gene expression at the chromatin level.
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Affiliation(s)
- Rosanna S Kwok
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
| | - Vu H Lam
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
| | - Joanna C Chiu
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
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18
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Andreazza S, Bouleau S, Martin B, Lamouroux A, Ponien P, Papin C, Chélot E, Jacquet E, Rouyer F. Daytime CLOCK Dephosphorylation Is Controlled by STRIPAK Complexes in Drosophila. Cell Rep 2015; 11:1266-79. [PMID: 25981041 DOI: 10.1016/j.celrep.2015.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 02/23/2015] [Accepted: 04/16/2015] [Indexed: 11/29/2022] Open
Abstract
In the Drosophila circadian oscillator, the CLOCK/CYCLE complex activates transcription of period (per) and timeless (tim) in the evening. PER and TIM proteins then repress CLOCK (CLK) activity during the night. The pace of the oscillator depends upon post-translational regulation that affects both positive and negative components of the transcriptional loop. CLK protein is highly phosphorylated and inactive in the morning, whereas hypophosphorylated active forms are present in the evening. How this critical dephosphorylation step is mediated is unclear. We show here that two components of the STRIPAK complex, the CKA regulatory subunit of the PP2A phosphatase and its interacting protein STRIP, promote CLK dephosphorylation during the daytime. In contrast, the WDB regulatory PP2A subunit stabilizes CLK without affecting its phosphorylation state. Inhibition of the PP2A catalytic subunit and CKA downregulation affect daytime CLK similarly, suggesting that STRIPAK complexes are the main PP2A players in producing transcriptionally active hypophosphorylated CLK.
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Affiliation(s)
- Simonetta Andreazza
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sylvina Bouleau
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Béatrice Martin
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Annie Lamouroux
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, 91190 Gif-sur-Yvette, France
| | - Christian Papin
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Elisabeth Chélot
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, 91190 Gif-sur-Yvette, France
| | - François Rouyer
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France.
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19
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Tataroglu O, Emery P. The molecular ticks of the Drosophila circadian clock. CURRENT OPINION IN INSECT SCIENCE 2015; 7:51-57. [PMID: 26120561 PMCID: PMC4480617 DOI: 10.1016/j.cois.2015.01.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Drosophila is a powerful model to understand the mechanisms underlying circadian rhythms. The Drosophila molecular clock is comprised of transcriptional feedback loops. The expressions of the critical transcriptional activator CLK and its repressors PER and TIM are under tight transcriptional control. However, posttranslational modification of these proteins and regulation of their stability are critical to their function and to the generation of 24-hr period rhythms. We review here recent progress made in our understanding of PER, TIM and CLK posttranslational control. We also review recent studies that are uncovering the importance of novel regulatory mechanisms that affect mRNA stability and translation of circadian pacemaker proteins and their output.
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20
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Li Q, Wang Z, Lian J, Schiøtt M, Jin L, Zhang P, Zhang Y, Nygaard S, Peng Z, Zhou Y, Deng Y, Zhang W, Boomsma JJ, Zhang G. Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior. Nat Commun 2014; 5:4943. [PMID: 25266559 PMCID: PMC4200514 DOI: 10.1038/ncomms5943] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 08/08/2014] [Indexed: 01/16/2023] Open
Abstract
Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome. Recent studies suggest that RNA editing might enhance the diversity of gene products at the post-transcriptional level, particularly to induce functional changes in the nervous system. Using head samples from the leaf-cutting ant Acromyrmex echinatior, we compare RNA editomes across eusocial castes, identifying ca. 11,000 RNA editing sites in gynes, large workers and small workers. Those editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis. Most A. echinatior editing sites are species specific, but 8–23% are conserved across ant subfamilies and likely to have been important for the evolution of eusociality in ants. The level of editing varies for the same site between castes, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants. Post-translational mRNA editing has the potential to enhance the diversity of gene products and alter the functional properties of proteins. Here, Li et al. provide evidence that RNA editing is involved in generating caste-specific contrasting phenotypes in the leaf-cutting ant Acromyrmex echinatior.
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Affiliation(s)
- Qiye Li
- 1] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China [2] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zongji Wang
- 1] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China [2] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Jinmin Lian
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Lijun Jin
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Pei Zhang
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | | | - Sanne Nygaard
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | | | - Yang Zhou
- 1] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China [2] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yuan Deng
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | | | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Guojie Zhang
- 1] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China [2] Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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21
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Lee E, Jeong EH, Jeong HJ, Yildirim E, Vanselow JT, Ng F, Liu Y, Mahesh G, Kramer A, Hardin PE, Edery I, Kim EY. Phosphorylation of a central clock transcription factor is required for thermal but not photic entrainment. PLoS Genet 2014; 10:e1004545. [PMID: 25121504 PMCID: PMC4133166 DOI: 10.1371/journal.pgen.1004545] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/17/2014] [Indexed: 01/04/2023] Open
Abstract
Transcriptional/translational feedback loops drive daily cycles of expression in clock genes and clock-controlled genes, which ultimately underlie many of the overt circadian rhythms manifested by organisms. Moreover, phosphorylation of clock proteins plays crucial roles in the temporal regulation of clock protein activity, stability and subcellular localization. dCLOCK (dCLK), the master transcription factor driving cyclical gene expression and the rate-limiting component in the Drosophila circadian clock, undergoes daily changes in phosphorylation. However, the physiological role of dCLK phosphorylation is not clear. Using a Drosophila tissue culture system, we identified multiple phosphorylation sites on dCLK. Expression of a mutated version of dCLK where all the mapped phospho-sites were switched to alanine (dCLK-15A) rescues the arrythmicity of Clkout flies, yet with an approximately 1.5 hr shorter period. The dCLK-15A protein attains substantially higher levels in flies compared to the control situation, and also appears to have enhanced transcriptional activity, consistent with the observed higher peak values and amplitudes in the mRNA rhythms of several core clock genes. Surprisingly, the clock-controlled daily activity rhythm in dCLK-15A expressing flies does not synchronize properly to daily temperature cycles, although there is no defect in aligning to light/dark cycles. Our findings suggest a novel role for clock protein phosphorylation in governing the relative strengths of entraining modalities by adjusting the dynamics of circadian gene expression. Circadian clocks are synchronized to local time by daily cycles in light-dark and temperature. Although light is generally thought to be the most dominant entraining cue in nature, daily cycles in temperature are sufficient to synchronize clocks in a large range of organisms. In Drosophila, dCLOCK is a master circadian transcription factor that drives cyclical gene expression and is likely the rate-limiting component in the transcriptional/translational feedback loops that underlie the timekeeping mechanism. dCLOCK undergoes temporal changes in phosphorylation throughout a day, which is also observed for mammalian CLOCK. However, the role of CLOCK phosphorylation at the organismal level is still unclear. Using mass-spectrometry, we identified more than a dozen phosphorylation sites on dCLOCK. Blocking global phosphorylation of dCLOCK by mutating phospho-acceptor sites to alanine increases its abundance and transcriptional activity, leading to higher peak values and amplitudes in the mRNA rhythms of core clock genes, which likely explains the accelerated clock speed. Surprisingly, the clock-controlled daily activity rhythm fails to maintain synchrony with daily temperature cycles, although there is no observable defect in aligning to light/dark cycles. Our findings suggest a novel role for clock protein phosphorylation in governing the effective strengths of entraining modalities by adjusting clock amplitude.
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Affiliation(s)
- Euna Lee
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
| | - Eun Hee Jeong
- Department of Brain Science, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
| | - Hyun-Jeong Jeong
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
| | - Evrim Yildirim
- Department of Molecular Biology and Biochemistry, Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, United States of America
| | - Jens T. Vanselow
- Laboratory of Chronobiology, Charité–Universitätsmedizin, Berlin, Germany
| | - Fanny Ng
- Texas A&M University Department of Biology and Center for Biological Clocks Research, College Station, Texas, United States of America
| | - Yixiao Liu
- Texas A&M University Department of Biology and Center for Biological Clocks Research, College Station, Texas, United States of America
| | - Guruswamy Mahesh
- Texas A&M University Department of Biology and Center for Biological Clocks Research, College Station, Texas, United States of America
| | - Achim Kramer
- Laboratory of Chronobiology, Charité–Universitätsmedizin, Berlin, Germany
| | - Paul E. Hardin
- Texas A&M University Department of Biology and Center for Biological Clocks Research, College Station, Texas, United States of America
| | - Isaac Edery
- Department of Molecular Biology and Biochemistry, Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, United States of America
- * E-mail: (IE); (EYK)
| | - Eun Young Kim
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- * E-mail: (IE); (EYK)
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22
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Gossan NC, Zhang F, Guo B, Jin D, Yoshitane H, Yao A, Glossop N, Zhang YQ, Fukada Y, Meng QJ. The E3 ubiquitin ligase UBE3A is an integral component of the molecular circadian clock through regulating the BMAL1 transcription factor. Nucleic Acids Res 2014; 42:5765-75. [PMID: 24728990 PMCID: PMC4027211 DOI: 10.1093/nar/gku225] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/02/2014] [Accepted: 03/06/2014] [Indexed: 11/28/2022] Open
Abstract
Post-translational modifications (such as ubiquitination) of clock proteins are critical in maintaining the precision and robustness of the evolutionarily conserved circadian clock. Ubiquitination of the core clock transcription factor BMAL1 (brain and muscle Arnt-like 1) has recently been reported. However, it remains unknown whether BMAL1 ubiquitination affects circadian pacemaking and what ubiquitin ligase(s) is involved. Here, we show that activating UBE3A (by expressing viral oncogenes E6/E7) disrupts circadian oscillations in mouse embryonic fibroblasts, measured using PER2::Luc dynamics, and rhythms in endogenous messenger ribonucleic acid and protein levels of BMAL1. Over-expression of E6/E7 reduced the level of BMAL1, increasing its ubiquitination and proteasomal degradation. UBE3A could bind to and degrade BMAL1 in a ubiquitin ligase-dependent manner. This occurred both in the presence and absence of E6/E7. We provide in vitro (knockdown/over-expression in mammalian cells) and in vivo (genetic manipulation in Drosophila) evidence for an endogenous role of UBE3A in regulating circadian dynamics and rhythmic locomotor behaviour. Together, our data reveal an essential and conserved role of UBE3A in the regulation of the circadian system in mammals and flies and identify a novel mechanistic link between oncogene E6/E7-mediated cell transformation and circadian (BMAL1) disruption.
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Affiliation(s)
- Nicole C Gossan
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Feng Zhang
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Baoqiang Guo
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Ding Jin
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Hikari Yoshitane
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Aiyu Yao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Nick Glossop
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Yong Q Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yoshitaka Fukada
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Qing-Jun Meng
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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23
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Seluzicki A, Flourakis M, Kula-Eversole E, Zhang L, Kilman V, Allada R. Dual PDF signaling pathways reset clocks via TIMELESS and acutely excite target neurons to control circadian behavior. PLoS Biol 2014; 12:e1001810. [PMID: 24643294 PMCID: PMC3958333 DOI: 10.1371/journal.pbio.1001810] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 02/05/2014] [Indexed: 12/20/2022] Open
Abstract
Molecular circadian clocks are interconnected via neural networks. In Drosophila, PIGMENT-DISPERSING FACTOR (PDF) acts as a master network regulator with dual functions in synchronizing molecular oscillations between disparate PDF(+) and PDF(-) circadian pacemaker neurons and controlling pacemaker neuron output. Yet the mechanisms by which PDF functions are not clear. We demonstrate that genetic inhibition of protein kinase A (PKA) in PDF(-) clock neurons can phenocopy PDF mutants while activated PKA can partially rescue PDF receptor mutants. PKA subunit transcripts are also under clock control in non-PDF DN1p neurons. To address the core clock target of PDF, we rescued per in PDF neurons of arrhythmic per⁰¹ mutants. PDF neuron rescue induced high amplitude rhythms in the clock component TIMELESS (TIM) in per-less DN1p neurons. Complete loss of PDF or PKA inhibition also results in reduced TIM levels in non-PDF neurons of per⁰¹ flies. To address how PDF impacts pacemaker neuron output, we focally applied PDF to DN1p neurons and found that it acutely depolarizes and increases firing rates of DN1p neurons. Surprisingly, these effects are reduced in the presence of an adenylate cyclase inhibitor, yet persist in the presence of PKA inhibition. We have provided evidence for a signaling mechanism (PKA) and a molecular target (TIM) by which PDF resets and synchronizes clocks and demonstrates an acute direct excitatory effect of PDF on target neurons to control neuronal output. The identification of TIM as a target of PDF signaling suggests it is a multimodal integrator of cell autonomous clock, environmental light, and neural network signaling. Moreover, these data reveal a bifurcation of PKA-dependent clock effects and PKA-independent output effects. Taken together, our results provide a molecular and cellular basis for the dual functions of PDF in clock resetting and pacemaker output.
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Affiliation(s)
- Adam Seluzicki
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Matthieu Flourakis
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Elzbieta Kula-Eversole
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Luoying Zhang
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Valerie Kilman
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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Szabó Á, Papin C, Zorn D, Ponien P, Weber F, Raabe T, Rouyer F. The CK2 kinase stabilizes CLOCK and represses its activity in the Drosophila circadian oscillator. PLoS Biol 2013; 11:e1001645. [PMID: 24013921 PMCID: PMC3754892 DOI: 10.1371/journal.pbio.1001645] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/19/2013] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation is a pivotal regulatory mechanism for protein stability and activity in circadian clocks regardless of their evolutionary origin. It determines the speed and strength of molecular oscillations by acting on transcriptional activators and their repressors, which form negative feedback loops. In Drosophila, the CK2 kinase phosphorylates and destabilizes the PERIOD (PER) and TIMELESS (TIM) proteins, which inhibit CLOCK (CLK) transcriptional activity. Here we show that CK2 also targets the CLK activator directly. Downregulating the activity of the catalytic α subunit of CK2 induces CLK degradation, even in the absence of PER and TIM. Unexpectedly, the regulatory β subunit of the CK2 holoenzyme is not required for the regulation of CLK stability. In addition, downregulation of CK2α activity decreases CLK phosphorylation and increases per and tim transcription. These results indicate that CK2 inhibits CLK degradation while reducing its activity. Since the CK1 kinase promotes CLK degradation, we suggest that CLK stability and transcriptional activity result from counteracting effects of CK1 and CK2.
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Affiliation(s)
- Áron Szabó
- Institut de Neurobiologie Alfred Fessard, Centre National de la Recherche Scientifique Unité Propre de Recherche 3294, Gif-sur-Yvette, France
- Département de Biologie, Université Paris Sud, Orsay, France
| | - Christian Papin
- Institut de Neurobiologie Alfred Fessard, Centre National de la Recherche Scientifique Unité Propre de Recherche 3294, Gif-sur-Yvette, France
- Département de Biologie, Université Paris Sud, Orsay, France
| | - Daniela Zorn
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Gif-sur-Yvette, France
- IMAGIF, Centre de Recherche de Gif, Gif-sur-Yvette, France
| | - Frank Weber
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | - Thomas Raabe
- University of Wuerzburg, Institute of Medical Radiation and Cell Research, Wuerzburg, Germany
| | - François Rouyer
- Institut de Neurobiologie Alfred Fessard, Centre National de la Recherche Scientifique Unité Propre de Recherche 3294, Gif-sur-Yvette, France
- Département de Biologie, Université Paris Sud, Orsay, France
- * E-mail:
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25
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Hardin PE, Panda S. Circadian timekeeping and output mechanisms in animals. Curr Opin Neurobiol 2013; 23:724-31. [PMID: 23731779 DOI: 10.1016/j.conb.2013.02.018] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 11/26/2022]
Abstract
Daily rhythms in animal behavior, physiology and metabolism are driven by cell-autonomous clocks that are synchronized by environmental cycles, but maintain ∼24 hours rhythms even in the absence of environmental cues. These clocks keep time and control overt rhythms via interlocked transcriptional feedback loops, making it imperative to define the mechanisms that drive rhythmic transcription within these loops and on a genome-wide scale. Recent work identifies novel post-transcriptional and post-translational mechanisms that govern progression through these feedback loops to maintain a period of ∼24 hours. Likewise, new microarray and deep sequencing studies reveal interplay among clock activators, chromatin remodeling and RNA Pol II binding to set the phase of gene transcription and drive post-transcriptional regulatory systems that may greatly increase the proportion of genes that are under clock control. Despite great progress, gaps in our understanding of how feedback loop transcriptional programs maintain ∼24 hours cycles and drive overt rhythms remain.
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Affiliation(s)
- Paul E Hardin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, United States.
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Yoshii T, Rieger D, Helfrich-Förster C. Two clocks in the brain. PROGRESS IN BRAIN RESEARCH 2012; 199:59-82. [DOI: 10.1016/b978-0-444-59427-3.00027-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Özkaya Ö, Rosato E. The Circadian Clock of the Fly: A Neurogenetics Journey Through Time. GENE-ENVIRONMENT INTERPLAY 2012; 77:79-123. [DOI: 10.1016/b978-0-12-387687-4.00004-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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HSP90 functions in the circadian clock through stabilization of the client F-box protein ZEITLUPE. Proc Natl Acad Sci U S A 2011; 108:16843-8. [PMID: 21949396 DOI: 10.1073/pnas.1110406108] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The autoregulatory loops of the circadian clock consist of feedback regulation of transcription/translation circuits but also require finely coordinated cytoplasmic and nuclear proteostasis. Although protein degradation is important to establish steady-state levels, maturation into their active conformation also factors into protein homeostasis. HSP90 facilitates the maturation of a wide range of client proteins, and studies in metazoan clocks implicate HSP90 as an integrator of input or output. Here we show that the Arabidopsis circadian clock-associated F-box protein ZEITLUPE (ZTL) is a unique client for cytoplasmic HSP90. The HSP90-specific inhibitor geldanamycin and RNAi-mediated depletion of cytoplasmic HSP90 reduces levels of ZTL and lengthens circadian period, consistent with ztl loss-of-function alleles. Transient transfection of artificial microRNA targeting cytoplasmic HSP90 genes similarly lengthens period. Proteolytic targets of SCF(ZTL), TOC1 and PRR5, are stabilized in geldanamycin-treated seedlings, whereas the levels of closely related clock proteins, PRR3 and PRR7, are unchanged. An in vitro holdase assay, typically used to demonstrate chaperone activity, shows that ZTL can be effectively bound, and aggregation prevented, by HSP90. GIGANTEA, a unique stabilizer of ZTL, may act in the same pathway as HSP90, possibly linking these two proteins to a similar mechanism. Our findings establish maturation of ZTL by HSP90 as essential for proper function of the Arabidopsis circadian clock. Unlike metazoan systems, HSP90 functions here within the core oscillator. Additionally, F-box proteins as clients may place HSP90 in a unique and more central role in proteostasis.
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Weber F, Zorn D, Rademacher C, Hung HC. Post-translational timing mechanisms of the Drosophila circadian clock. FEBS Lett 2011; 585:1443-9. [PMID: 21486567 DOI: 10.1016/j.febslet.2011.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 03/29/2011] [Accepted: 04/04/2011] [Indexed: 11/20/2022]
Abstract
Circadian clocks allow a temporal coordination and segregation of physiological, metabolic, and behavioural processes as well as their synchronization with the environmental cycles of day and night. Circadian regulation thereby provides a vital advantage, improving an organisms' adaptation to its environment. The molecular clock can be synchronized with environmental cycles of day and night, but is able to maintain a self-sustained molecular oscillation also in the absence of environmental stimuli. Interlocked transcriptional-translational feedback loops were shown to form the basis of circadian clock function in all phyla from bacteria, fungi, plants, insects to humans. More recently post-translational regulation was identified to be equally important, if not sufficient for molecular clock function and accurate timing of circadian transcription. Here we review recent insights into post-translational timing mechanisms that control the circadian clock, with a particular focus on Drosophila. Analogous to transcriptional feedback regulation, circadian clock function in Drosophila appears to rely on inter-connected post-translational timers. Post-translational regulation of clock proteins illustrates mechanisms that allow a precise temporal control of transcription factors in general and of circadian transcription in particular.
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Affiliation(s)
- Frank Weber
- University of Heidelberg Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
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