1
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Gul S, Aydin C, Ozcan O, Gurkan B, Surme S, Baris I, Kavakli IH. The Arg-293 of Cryptochrome1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm. J Biol Chem 2020; 295:17187-17199. [PMID: 33028638 PMCID: PMC7863883 DOI: 10.1074/jbc.ra120.014333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/01/2020] [Indexed: 11/06/2022] Open
Abstract
Mammalian circadian clocks are driven by transcription/translation feedback loops composed of positive transcriptional activators (BMAL1 and CLOCK) and negative repressors (CRYPTOCHROMEs (CRYs) and PERIODs (PERs)). CRYs, in complex with PERs, bind to the BMAL1/CLOCK complex and repress E-box-driven transcription of clock-associated genes. There are two individual CRYs, with CRY1 exhibiting higher affinity to the BMAL1/CLOCK complex than CRY2. It is known that this differential binding is regulated by a dynamic serine-rich loop adjacent to the secondary pocket of both CRYs, but the underlying features controlling loop dynamics are not known. Here we report that allosteric regulation of the serine-rich loop is mediated by Arg-293 of CRY1, identified as a rare CRY1 SNP in the Ensembl and 1000 Genomes databases. The p.Arg293His CRY1 variant caused a shortened circadian period in a Cry1-/-Cry2-/- double knockout mouse embryonic fibroblast cell line. Moreover, the variant displayed reduced repressor activity on BMAL1/CLOCK driven transcription, which is explained by reduced affinity to BMAL1/CLOCK in the absence of PER2 compared with CRY1. Molecular dynamics simulations revealed that the p.Arg293His CRY1 variant altered a communication pathway between Arg-293 and the serine loop by reducing its dynamicity. Collectively, this study provides direct evidence that allosterism in CRY1 is critical for the regulation of circadian rhythm.
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Affiliation(s)
- Seref Gul
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Cihan Aydin
- Department of Molecular Biology and Genetics, Istanbul Medeniyet University, Istanbul, Turkey
| | - Onur Ozcan
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Berke Gurkan
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Saliha Surme
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Ibrahim Baris
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey; Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
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2
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Parico GCG, Partch CL. The tail of cryptochromes: an intrinsically disordered cog within the mammalian circadian clock. Cell Commun Signal 2020; 18:182. [PMID: 33198762 PMCID: PMC7667820 DOI: 10.1186/s12964-020-00665-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Cryptochrome (CRY) proteins play an essential role in regulating mammalian circadian rhythms. CRY is composed of a structured N-terminal domain known as the photolyase homology region (PHR), which is tethered to an intrinsically disordered C-terminal tail. The PHR domain is a critical hub for binding other circadian clock components such as CLOCK, BMAL1, PERIOD, or the ubiquitin ligases FBXL3 and FBXL21. While the isolated PHR domain is necessary and sufficient to generate circadian rhythms, removing or modifying the cryptochrome tails modulates the amplitude and/or periodicity of circadian rhythms, suggesting that they play important regulatory roles in the molecular circadian clock. In this commentary, we will discuss how recent studies of these intrinsically disordered tails are helping to establish a general and evolutionarily conserved model for CRY function, where the function of PHR domains is modulated by reversible interactions with their intrinsically disordered tails. Video abstract
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Affiliation(s)
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, USA. .,Center for Circadian Biology, UC San Diego, La Jolla, USA.
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3
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Pelham JF, Dunlap JC, Hurley JM. Intrinsic disorder is an essential characteristic of components in the conserved circadian circuit. Cell Commun Signal 2020; 18:181. [PMID: 33176800 PMCID: PMC7656774 DOI: 10.1186/s12964-020-00658-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/06/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION The circadian circuit, a roughly 24 h molecular feedback loop, or clock, is conserved from bacteria to animals and allows for enhanced organismal survival by facilitating the anticipation of the day/night cycle. With circadian regulation reportedly impacting as high as 80% of protein coding genes in higher eukaryotes, the protein-based circadian clock broadly regulates physiology and behavior. Due to the extensive interconnection between the clock and other cellular systems, chronic disruption of these molecular rhythms leads to a decrease in organismal fitness as well as an increase of disease rates in humans. Importantly, recent research has demonstrated that proteins comprising the circadian clock network display a significant amount of intrinsic disorder. MAIN BODY In this work, we focus on the extent of intrinsic disorder in the circadian clock and its potential mechanistic role in circadian timing. We highlight the conservation of disorder by quantifying the extent of computationally-predicted protein disorder in the core clock of the key eukaryotic circadian model organisms Drosophila melanogaster, Neurospora crassa, and Mus musculus. We further examine previously published work, as well as feature novel experimental evidence, demonstrating that the core negative arm circadian period drivers FREQUENCY (Neurospora crassa) and PERIOD-2 (PER2) (Mus musculus), possess biochemical characteristics of intrinsically disordered proteins. Finally, we discuss the potential contributions of the inherent biophysical principals of intrinsically disordered proteins that may explain the vital mechanistic roles they play in the clock to drive their broad evolutionary conservation in circadian timekeeping. CONCLUSION The pervasive conservation of disorder amongst the clock in the crown eukaryotes suggests that disorder is essential for optimal circadian timing from fungi to animals, providing vital homeostatic cellular maintenance and coordinating organismal physiology across phylogenetic kingdoms. Video abstract.
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Affiliation(s)
- Jacqueline F. Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Jay C. Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Jennifer M. Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12018 USA
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4
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Parico GCG, Perez I, Fribourgh JL, Hernandez BN, Lee HW, Partch CL. The human CRY1 tail controls circadian timing by regulating its association with CLOCK:BMAL1. Proc Natl Acad Sci U S A 2020; 117:27971-27979. [PMID: 33106415 PMCID: PMC7668087 DOI: 10.1073/pnas.1920653117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Circadian rhythms are generated by interlocked transcription-translation feedback loops that establish cell-autonomous biological timing of ∼24 h. Mutations in core clock genes that alter their stability or affinity for one another lead to changes in circadian period. The human CRY1Δ11 mutant lengthens circadian period to cause delayed sleep phase disorder (DSPD), characterized by a very late onset of sleep. CRY1 is a repressor that binds to the transcription factor CLOCK:BMAL1 to inhibit its activity and close the core feedback loop. We previously showed how the PHR (photolyase homology region) domain of CRY1 interacts with distinct sites on CLOCK and BMAL1 to sequester the transactivation domain from coactivators. However, the Δ11 variant alters an intrinsically disordered tail in CRY1 downstream of the PHR. We show here that the CRY1 tail, and in particular the region encoded by exon 11, modulates the affinity of the PHR domain for CLOCK:BMAL1. The PHR-binding epitope in exon 11 is necessary and sufficient to disrupt the interaction between CRY1 and the subunit CLOCK. Moreover, PHR-tail interactions are conserved in the paralog CRY2 and reduced when either CRY is bound to the circadian corepressor PERIOD2. Discovery of this autoregulatory role for the mammalian CRY1 tail and conservation of PHR-tail interactions in both mammalian cryptochromes highlights functional conservation with plant and insect cryptochromes, which also utilize PHR-tail interactions to reversibly control their activity.
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Affiliation(s)
- Gian Carlo G Parico
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Ivette Perez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Britney N Hernandez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064;
- Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093
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5
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Partch CL. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. J Mol Biol 2020; 432:3426-3448. [DOI: 10.1016/j.jmb.2019.12.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
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6
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Identification of the Repressive Domain of the Negative Circadian Clock Component CHRONO. Int J Mol Sci 2020; 21:ijms21072469. [PMID: 32252431 PMCID: PMC7177903 DOI: 10.3390/ijms21072469] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 11/17/2022] Open
Abstract
Circadian rhythm is an endogenous, self-sustainable oscillation that participates in regulating organisms’ physiological activities. Key to this oscillation is a negative feedback by the main clock components Periods and Cryptochromes that repress the transcriptional activity of BMAL1/CLOCK (defined in the Abbreviations) complexes. In addition, a novel repressor, CHRONO, has been identified recently, but details of CHRONO’s function during repressing the circadian cycle remain unclear. Here we report that a domain of CHRONO mainly composed of α-helixes is critical to repression through the exploitation of protein–protein interactions according to luciferase reporter assays, co-immunoprecipitation, immunofluorescence, genome editing, and structural information analysis via circular dichroism spectroscopy. This repression is fulfilled by interactions between CHRONO and a region on the C-terminus of BMAL1 where Cryptochrome and CBP (defined in the Abbreviations) bind. Our resultsindicate that CHRONO and PER differentially function as BMAL1/CLOCK-dependent repressors. Besides, the N-terminus of CHRONO is important for its nuclear localization. We further develop a repression model of how PER, CRY, and CHRONO proteins associate with BMAL1, respectively.
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7
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Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife 2020; 9:e55275. [PMID: 32101164 PMCID: PMC7064333 DOI: 10.7554/elife.55275] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.
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Affiliation(s)
- Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California Santa CruzSanta CruzUnited States
| | | | | | - Alicia K Michael
- Department of Chemistry and Biochemistry, University of California Santa CruzSanta CruzUnited States
| | - Peter L Hsu
- Department of Pharmacology, University of WashingtonSeattleUnited States
| | - Christin Rakers
- Graduate School of Pharmaceutical Sciences, Kyoto UniversityKyotoJapan
| | - Leslee T Nguyen
- Department of Chemistry and Biochemistry, University of California Santa CruzSanta CruzUnited States
| | - Megan R Torgrimson
- Department of Chemistry and Biochemistry, University of California Santa CruzSanta CruzUnited States
| | - Gian Carlo G Parico
- Department of Chemistry and Biochemistry, University of California Santa CruzSanta CruzUnited States
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa CruzSanta CruzUnited States
| | - Ning Zheng
- Department of Pharmacology, University of WashingtonSeattleUnited States
- Howard Hughes Medical InstituteSeattleUnited States
| | | | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya UniversityNagoyaJapan
| | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya UniversityNagoyaJapan
- Department of Physics, Nagoya UniversityNagoyaJapan
- RIKEN Center for Computational ScienceKobeJapan
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa CruzSanta CruzUnited States
- Center for Circadian Biology, University of California San DiegoLa JollaUnited States
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8
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Garg A, Orru R, Ye W, Distler U, Chojnacki JE, Köhn M, Tenzer S, Sönnichsen C, Wolf E. Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein. J Biol Chem 2019; 294:16604-16619. [PMID: 31515273 DOI: 10.1074/jbc.ra119.009845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
The mammalian CLOCK:BMAL1 transcription factor complex and its coactivators CREB-binding protein (CBP)/p300 and mixed-lineage leukemia 1 (MLL1) critically regulate circadian transcription and chromatin modification. Circadian oscillations are regulated by interactions of BMAL1's C-terminal transactivation domain (TAD) with the KIX domain of CBP/p300 (activating) and with the clock protein CRY1 (repressing) as well as by the BMAL1 G-region preceding the TAD. Circadian acetylation of Lys537 within the G-region enhances repressive BMAL1-TAD-CRY1 interactions. Here, we characterized the interaction of the CBP-KIX domain with BMAL1 proteins, including the BMAL1-TAD, parts of the G-region, and Lys537 Tethering the small compound 1-10 in the MLL-binding pocket of the CBP-KIX domain weakened BMAL1 binding, and MLL1-bound KIX did not form a ternary complex with BMAL1, indicating that the MLL-binding pocket is important for KIX-BMAL1 interactions. Small-angle X-ray scattering (SAXS) models of BMAL1 and BMAL1:KIX complexes revealed that the N-terminal BMAL1 G-region including Lys537 forms elongated extensions emerging from the bulkier BMAL1-TAD:KIX core complex. Fitting high-resolution KIX domain structures into the SAXS-derived envelopes suggested that the G-region emerges near the MLL-binding pocket, further supporting a role of this pocket in BMAL1 binding. Additionally, mutations in the second CREB-pKID/c-Myb-binding pocket of the KIX domain moderately impacted BMAL1 binding. The BMAL1(K537Q) mutation mimicking Lys537 acetylation, however, did not affect the KIX-binding affinity, in contrast to its enhancing effect on CRY1 binding. Our results significantly advance the mechanistic understanding of the protein interaction networks controlling CLOCK:BMAL1- and CBP-dependent gene regulation in the mammalian circadian clock.
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Affiliation(s)
- Archit Garg
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany.,Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, 55128 Mainz, Germany
| | - Roberto Orru
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, 55128 Mainz, Germany
| | - Weixiang Ye
- Institute of Physical Chemistry, Johannes Gutenberg-University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
| | | | - Maja Köhn
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
| | - Carsten Sönnichsen
- Institute of Physical Chemistry, Johannes Gutenberg-University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Eva Wolf
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany .,Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, 55128 Mainz, Germany
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9
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Dimova EY, Jakupovic M, Kubaichuk K, Mennerich D, Chi TF, Tamanini F, Oklejewicz M, Hänig J, Byts N, Mäkelä KA, Herzig KH, Koivunen P, Chaves I, van der Horst G, Kietzmann T. The Circadian Clock Protein CRY1 Is a Negative Regulator of HIF-1α. iScience 2019; 13:284-304. [PMID: 30875610 PMCID: PMC6416729 DOI: 10.1016/j.isci.2019.02.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 01/03/2019] [Accepted: 02/22/2019] [Indexed: 01/05/2023] Open
Abstract
The circadian clock and the hypoxia-signaling pathway are regulated by an integrated interplay of positive and negative feedback limbs that incorporate energy homeostasis and carcinogenesis. We show that the negative circadian regulator CRY1 is also a negative regulator of hypoxia-inducible factor (HIF). Mechanistically, CRY1 interacts with the basic-helix-loop-helix domain of HIF-1α via its tail region. Subsequently, CRY1 reduces HIF-1α half-life and binding of HIFs to target gene promoters. This appeared to be CRY1 specific because genetic disruption of CRY1, but not CRY2, affected the hypoxia response. Furthermore, CRY1 deficiency could induce cellular HIF levels, proliferation, and migration, which could be reversed by CRISPR/Cas9- or short hairpin RNA-mediated HIF knockout. Altogether, our study provides a mechanistic explanation for genetic association studies linking a disruption of the circadian clock with hypoxia-associated processes such as carcinogenesis.
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Affiliation(s)
- Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland.
| | - Mirza Jakupovic
- Department of Biochemistry, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Kateryna Kubaichuk
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Daniela Mennerich
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Tabughang Franklin Chi
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Filippo Tamanini
- Department of Molecular Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015CN Rotterdam, the Netherlands
| | - Małgorzata Oklejewicz
- Department of Molecular Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015CN Rotterdam, the Netherlands
| | - Jens Hänig
- Novartis Pharma GmbH, 97082 Würzburg, Germany
| | - Nadiya Byts
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Kari A Mäkelä
- Biocenter Oulu, Department of Physiology, University of Oulu, 90014 Oulu, Finland
| | - Karl-Heinz Herzig
- Biocenter Oulu, Department of Physiology, University of Oulu, 90014 Oulu, Finland
| | - Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Ines Chaves
- Department of Molecular Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015CN Rotterdam, the Netherlands
| | - Gijsbertus van der Horst
- Department of Molecular Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015CN Rotterdam, the Netherlands
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland.
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10
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Loros JJ. Principles of the animal molecular clock learned from Neurospora. Eur J Neurosci 2019; 51:19-33. [PMID: 30687965 DOI: 10.1111/ejn.14354] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 12/28/2022]
Abstract
Study of Neurospora, a model system evolutionarily related to animals and sharing a circadian system having nearly identical regulatory architecture to that of animals, has advanced our understanding of all circadian rhythms. Work on the molecular bases of the Oscillator began in Neurospora before any clock genes were cloned and provided the second example of a clock gene, frq, as well as the first direct experimental proof that the core of the Oscillator was built around a transcriptional translational negative feedback loop (TTFL). Proof that FRQ was a clock component provided the basis for understanding how light resets the clock, and this in turn provided the generally accepted understanding for how light resets all animal and fungal clocks. Experiments probing the mechanism of light resetting led to the first identification of a heterodimeric transcriptional activator as the positive element in a circadian feedback loop, and to the general description of the fungal/animal clock as a single step TTFL. The common means through which DNA damage impacts the Oscillator in fungi and animals was first described in Neurospora. Lastly, the systematic study of Output was pioneered in Neurospora, providing the vocabulary and conceptual framework for understanding how Output works in all cells. This model system has contributed to the current appreciation of the role of Intrinsic Disorder in clock proteins and to the documentation of the essential roles of protein post-translational modification, as distinct from turnover, in building a circadian clock.
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Affiliation(s)
- Jennifer J Loros
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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11
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Abstract
Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components. Posttranslational modifications and protein–protein interactions have become a recent focus, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. This review covers the structural aspects of circadian oscillators, and serves as a primer for this exciting realm of structural biology.
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Affiliation(s)
- Reena Saini
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Seth J Davis
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany. .,Department of Biology, University of York, York, UK.
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12
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Rosensweig C, Green CB. Periodicity, repression, and the molecular architecture of the mammalian circadian clock. Eur J Neurosci 2018; 51:139-165. [PMID: 30402960 DOI: 10.1111/ejn.14254] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/03/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
Abstract
Large molecular machines regulate daily cycles of transcriptional activity and help generate rhythmic behavior. In recent years, structural and biochemical analyses have elucidated a number of principles guiding the interactions of proteins that form the basis of circadian timing. In its simplest form, the circadian clock is composed of a transcription/translation feedback loop. However, this description elides a complicated process of activator recruitment, chromatin decompaction, recruitment of coactivators, expression of repressors, formation of a repressive complex, repression of the activators, and ultimately degradation of the repressors and reinitiation of the cycle. Understanding the core principles underlying the clock requires careful examination of molecular and even atomic level details of these processes. Here, we review major structural and biochemical findings in circadian biology and make the argument that shared protein interfaces within the clockwork are critical for both the generation of rhythmicity and timing of the clock.
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Affiliation(s)
- Clark Rosensweig
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
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13
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Rosensweig C, Reynolds KA, Gao P, Laothamatas I, Shan Y, Ranganathan R, Takahashi JS, Green CB. An evolutionary hotspot defines functional differences between CRYPTOCHROMES. Nat Commun 2018; 9:1138. [PMID: 29556064 PMCID: PMC5859286 DOI: 10.1038/s41467-018-03503-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/19/2018] [Indexed: 12/30/2022] Open
Abstract
Mammalian circadian clocks are driven by a transcription/translation feedback loop composed of positive regulators (CLOCK/BMAL1) and repressors (CRYPTOCHROME 1/2 (CRY1/2) and PER1/2). To understand the structural principles of regulation, we used evolutionary sequence analysis to identify co-evolving residues within the CRY/PHL protein family. Here we report the identification of an ancestral secondary cofactor-binding pocket as an interface in repressive CRYs, mediating regulation through direct interaction with CLOCK and BMAL1. Mutations weakening binding between CLOCK/BMAL1 and CRY1 lead to acceleration of the clock, suggesting that subtle sequence divergences at this site can modulate clock function. Divergence between CRY1 and CRY2 at this site results in distinct periodic output. Weaker interactions between CRY2 and CLOCK/BMAL1 at this pocket are strengthened by co-expression of PER2, suggesting that PER expression limits the length of the repressive phase in CRY2-driven rhythms. Overall, this work provides a model for the mechanism and evolutionary variation of clock regulatory mechanisms. The molecular mechanisms that define the periodicity or rate of the circadian clock are not well understood. Here the authors use a multidisciplinary approach and identify a mechanism for period regulation that depends on the affinity of the core clock proteins for one another.
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Affiliation(s)
- Clark Rosensweig
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.,Department of Neurobiology, Northwestern University, 2205 Tech Drive, Pancoe 2230, Evanston, IL, 60208, USA
| | - Kimberly A Reynolds
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,The Green Center for Systems Biology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
| | - Peng Gao
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Isara Laothamatas
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Yongli Shan
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Rama Ranganathan
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,The Green Center for Systems Biology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,The Center for the Physics of Evolving Systems, Biochemistry and Molecular Biology, The Institute for Molecular Engineering, University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.
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14
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Dunlap JC, Loros JJ. Just-So Stories and Origin Myths: Phosphorylation and Structural Disorder in Circadian Clock Proteins. Mol Cell 2017; 69:165-168. [PMID: 29276084 DOI: 10.1016/j.molcel.2017.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/19/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022]
Abstract
Some longstanding dogmas in the circadian field warrant reexamination in light of recent studies focused on the role of post-translational modifications and intrinsic disorder in core circadian clock proteins of mice and fungi. Such dogmas include the role of turnover in circadian feedback loops and the origin myths describing evolutionary relatedness among circadian clocks. In this Essay, the authors recapitulate recent findings on circadian clock protein regulation by taking an unconventional approach in the form of a dialog between Wizard and Apprentice.
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Affiliation(s)
- Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755.
| | - Jennifer J Loros
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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15
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Understanding CRY2 interactions for optical control of intracellular signaling. Nat Commun 2017; 8:547. [PMID: 28916751 PMCID: PMC5601944 DOI: 10.1038/s41467-017-00648-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/17/2017] [Indexed: 01/19/2023] Open
Abstract
Arabidopsis cryptochrome 2 (CRY2) can simultaneously undergo light-dependent CRY2–CRY2 homo-oligomerization and CRY2–CIB1 hetero-dimerization, both of which have been widely used to optically control intracellular processes. Applications using CRY2–CIB1 interaction desire minimal CRY2 homo-oligomerization to avoid unintended complications, while those utilizing CRY2–CRY2 interaction prefer robust homo-oligomerization. However, selecting the type of CRY2 interaction has not been possible as the molecular mechanisms underlying CRY2 interactions are unknown. Here we report CRY2–CIB1 and CRY2–CRY2 interactions are governed by well-separated protein interfaces at the two termini of CRY2. N-terminal charges are critical for CRY2–CIB1 interaction. Moreover, two C-terminal charges impact CRY2 homo-oligomerization, with positive charges facilitating oligomerization and negative charges inhibiting it. By engineering C-terminal charges, we develop CRY2high and CRY2low with elevated or suppressed oligomerization respectively, which we use to tune the levels of Raf/MEK/ERK signaling. These results contribute to our understanding of the mechanisms underlying light-induced CRY2 interactions and enhance the controllability of CRY2-based optogenetic systems. Cryptochrome 2 (CRY2) can form light-regulated CRY2-CRY2 homo-oligomers or CRY2-CIB1 hetero-dimers, but modulating these interactions is difficult owing to the lack of interaction mechanism. Here the authors identify the interactions facilitating homo-oligomers and introduce mutations to create low and high oligomerization versions.
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16
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Vertebrate-like CRYPTOCHROME 2 from monarch regulates circadian transcription via independent repression of CLOCK and BMAL1 activity. Proc Natl Acad Sci U S A 2017; 114:E7516-E7525. [PMID: 28831003 DOI: 10.1073/pnas.1702014114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Circadian repression of CLOCK-BMAL1 by PERIOD and CRYPTOCHROME (CRY) in mammals lies at the core of the circadian timekeeping mechanism. CRY repression of CLOCK-BMAL1 and regulation of circadian period are proposed to rely primarily on competition for binding with coactivators on an α-helix located within the transactivation domain (TAD) of the BMAL1 C terminus. This model has, however, not been tested in vivo. Here, we applied CRISPR/Cas9-mediated mutagenesis in the monarch butterfly (Danaus plexippus), which possesses a vertebrate-like CRY (dpCRY2) and an ortholog of BMAL1, to show that insect CRY2 regulates circadian repression through TAD α-helix-dependent and -independent mechanisms. Monarch mutants lacking the BMAL1 C terminus including the TAD exhibited arrhythmic eclosion behavior. In contrast, mutants lacking the TAD α-helix but retaining the most distal C-terminal residues exhibited robust rhythms during the first day of constant darkness (DD1), albeit with a delayed peak of eclosion. Phase delay in this mutant on DD1 was exacerbated in the presence of a single functional allele of dpCry2, and rhythmicity was abolished in the absence of dpCRY2. Reporter assays in Drosophila S2 cells further revealed that dpCRY2 represses through two distinct mechanisms: a TAD-dependent mechanism that involves the dpBMAL1 TAD α-helix and dpCLK W328 and a TAD-independent mechanism involving dpCLK E333. Together, our results provide evidence for independent mechanisms of vertebrate-like CRY circadian regulation on the BMAL1 C terminus and the CLK PAS-B domain and demonstrate the importance of a BMAL1 TAD-independent mechanism for generating circadian rhythms in vivo.
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17
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Patke A, Murphy PJ, Onat OE, Krieger AC, Özçelik T, Campbell SS, Young MW. Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder. Cell 2017; 169:203-215.e13. [PMID: 28388406 DOI: 10.1016/j.cell.2017.03.027] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/18/2017] [Accepted: 03/20/2017] [Indexed: 12/12/2022]
Abstract
Patterns of daily human activity are controlled by an intrinsic circadian clock that promotes ∼24 hr rhythms in many behavioral and physiological processes. This system is altered in delayed sleep phase disorder (DSPD), a common form of insomnia in which sleep episodes are shifted to later times misaligned with the societal norm. Here, we report a hereditary form of DSPD associated with a dominant coding variation in the core circadian clock gene CRY1, which creates a transcriptional inhibitor with enhanced affinity for circadian activator proteins Clock and Bmal1. This gain-of-function CRY1 variant causes reduced expression of key transcriptional targets and lengthens the period of circadian molecular rhythms, providing a mechanistic link to DSPD symptoms. The allele has a frequency of up to 0.6%, and reverse phenotyping of unrelated families corroborates late and/or fragmented sleep patterns in carriers, suggesting that it affects sleep behavior in a sizeable portion of the human population.
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Affiliation(s)
- Alina Patke
- Laboratory of Genetics, The Rockefeller University, New York, NY 10065, USA.
| | - Patricia J Murphy
- Laboratory of Human Chronobiology, Weill Cornell Medical College, White Plains, NY 10605, USA
| | - Onur Emre Onat
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Ana C Krieger
- Department of Medicine, Center for Sleep Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Tayfun Özçelik
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Scott S Campbell
- Laboratory of Human Chronobiology, Weill Cornell Medical College, White Plains, NY 10605, USA
| | - Michael W Young
- Laboratory of Genetics, The Rockefeller University, New York, NY 10065, USA.
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18
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Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proc Natl Acad Sci U S A 2017; 114:1560-1565. [PMID: 28143926 DOI: 10.1073/pnas.1615310114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.
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19
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Abstract
There is a dynamic interplay between metabolic processes and gene regulation via the remodeling of chromatin. Most chromatin-modifying enzymes use cofactors, which are products of metabolic processes. This article explores the biosynthetic pathways of the cofactors nicotinamide adenine dinucleotide (NAD), acetyl coenzyme A (acetyl-CoA), S-adenosyl methionine (SAM), α-ketoglutarate, and flavin adenine dinucleotide (FAD), and their role in metabolically regulating chromatin processes. A more detailed look at the interaction between chromatin and the metabolic processes of circadian rhythms and aging is described as a paradigm for this emerging interdisciplinary field.
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Affiliation(s)
- Shelley L Berger
- Department of Cell & Developmental Biology, Department of Biology, and Department of Genetics, Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6508
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-4049
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20
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Shi G, Xie P, Qu Z, Zhang Z, Dong Z, An Y, Xing L, Liu Z, Dong Y, Xu G, Yang L, Liu Y, Xu Y. Distinct Roles of HDAC3 in the Core Circadian Negative Feedback Loop Are Critical for Clock Function. Cell Rep 2016; 14:823-834. [PMID: 26776516 DOI: 10.1016/j.celrep.2015.12.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/11/2015] [Accepted: 12/15/2015] [Indexed: 01/30/2023] Open
Abstract
In the core mammalian circadian negative feedback loop, the BMAL1-CLOCK complex activates the transcription of the genes Period (Per) and Cryptochrome (Cry). To close the negative feedback loop, the PER-CRY complex interacts with the BMAL1-CLOCK complex to repress its activity. These two processes are separated temporally to ensure clock function. Here, we show that histone deacetylase 3 (HDAC3) is a critical component of the circadian negative feedback loop by regulating both the activation and repression processes in a deacetylase activity-independent manner. Genetic depletion of Hdac3 results in low-amplitude circadian rhythms and dampened E-box-driven transcription. In subjective morning, HDAC3 is required for the efficient transcriptional activation process by regulating BMAL1 stability. In subjective night, however, HDAC3 blocks FBXL3-mediated CRY1 degradation and strongly promotes BMAL1 and CRY1 association. Therefore, these two opposing but temporally separated roles of HDAC3 in the negative feedback loop provide a mechanism for robust circadian gene expression.
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Affiliation(s)
- Guangsen Shi
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Pancheng Xie
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhipeng Qu
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhihui Zhang
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhen Dong
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Yang An
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Lijuan Xing
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Yingying Dong
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Guoqiang Xu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Ling Yang
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ying Xu
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China; Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.
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21
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Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. Cancer/Testis Antigen PASD1 Silences the Circadian Clock. Mol Cell 2015; 58:743-54. [PMID: 25936801 PMCID: PMC4458219 DOI: 10.1016/j.molcel.2015.03.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 02/13/2015] [Accepted: 03/25/2015] [Indexed: 01/06/2023]
Abstract
The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms.
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Affiliation(s)
- Alicia K Michael
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Stacy L Harvey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patrick J Sammons
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Amanda P Anderson
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Hema M Kopalle
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alison H Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, San Diego, CA 92093, USA.
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22
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Xu H, Gustafson CL, Sammons PJ, Khan SK, Parsley NC, Ramanathan C, Lee HW, Liu AC, Partch CL. Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C terminus. Nat Struct Mol Biol 2015; 22:476-484. [PMID: 25961797 PMCID: PMC4456216 DOI: 10.1038/nsmb.3018] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 04/03/2015] [Indexed: 12/14/2022]
Abstract
The molecular circadian clock in mammals is generated from transcriptional activation by the bHLH-PAS transcription factor CLOCK-BMAL1 and subsequent repression by PERIOD and CRYPTOCHROME (CRY). The mechanism by which CRYs repress CLOCK-BMAL1 to close the negative feedback loop and generate 24-h timing is not known. Here we show that, in mouse fibroblasts, CRY1 competes for binding with coactivators to the intrinsically unstructured C-terminal transactivation domain (TAD) of BMAL1 to establish a functional switch between activation and repression of CLOCK-BMAL1. TAD mutations that alter affinities for co-regulators affect the balance of repression and activation to consequently change the intrinsic circadian period or eliminate cycling altogether. Our results suggest that CRY1 fulfills its role as an essential circadian repressor by sequestering the TAD from coactivators, and they highlight regulation of the BMAL1 TAD as a critical mechanism for establishing circadian timing.
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Affiliation(s)
- Haiyan Xu
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee USA
- Feinstone Center for Genomic Research, University of Memphis, Memphis, Tennessee USA
| | - Chelsea L Gustafson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California USA
| | - Patrick J Sammons
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California USA
| | - Sanjoy K Khan
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee USA
| | - Nicole C Parsley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California USA
| | | | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California USA
| | - Andrew C Liu
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee USA
- Feinstone Center for Genomic Research, University of Memphis, Memphis, Tennessee USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California USA
- Center for Circadian Biology, University of California San Diego, San Diego, California USA
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23
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How is the inner circadian clock controlled by interactive clock proteins?: Structural analysis of clock proteins elucidates their physiological role. FEBS Lett 2015; 589:1516-29. [PMID: 25999309 DOI: 10.1016/j.febslet.2015.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 12/12/2022]
Abstract
Most internationally travelled researchers will have encountered jetlag. If not, working odd hours makes most of us feel somehow dysfunctional. How can all this be linked to circadian rhythms and circadian clocks? In this review, we define circadian clocks, their composition and underlying molecular mechanisms. We describe and discuss recent crystal structures of Drosophila and mammalian core clock components and the enormous impact they had on the understanding of circadian clock mechanisms. Finally, we highlight the importance of circadian clocks for the daily regulation of human/mammalian physiology and show connections to overall fitness, health and disease.
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24
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Papp SJ, Huber AL, Jordan SD, Kriebs A, Nguyen M, Moresco JJ, Yates JR, Lamia KA. DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization. eLife 2015; 4. [PMID: 25756610 PMCID: PMC4352707 DOI: 10.7554/elife.04883] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/10/2015] [Indexed: 11/13/2022] Open
Abstract
The circadian transcriptional repressors cryptochrome 1 (Cry1) and 2 (Cry2) evolved from photolyases, bacterial light-activated DNA repair enzymes. In this study, we report that while they have lost DNA repair activity, Cry1/2 adapted to protect genomic integrity by responding to DNA damage through posttranslational modification and coordinating the downstream transcriptional response. We demonstrate that genotoxic stress stimulates Cry1 phosphorylation and its deubiquitination by Herpes virus associated ubiquitin-specific protease (Hausp, a.k.a Usp7), stabilizing Cry1 and shifting circadian clock time. DNA damage also increases Cry2 interaction with Fbxl3, destabilizing Cry2. Thus, genotoxic stress increases the Cry1/Cry2 ratio, suggesting distinct functions for Cry1 and Cry2 following DNA damage. Indeed, the transcriptional response to genotoxic stress is enhanced in Cry1-/- and blunted in Cry2-/- cells. Furthermore, Cry2-/- cells accumulate damaged DNA. These results suggest that Cry1 and Cry2, which evolved from DNA repair enzymes, protect genomic integrity via coordinated transcriptional regulation.
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Affiliation(s)
- Stephanie J Papp
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Anne-Laure Huber
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Sabine D Jordan
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Anna Kriebs
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Madelena Nguyen
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Katja A Lamia
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
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25
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Crane BR, Young MW. Interactive features of proteins composing eukaryotic circadian clocks. Annu Rev Biochem 2015; 83:191-219. [PMID: 24905781 DOI: 10.1146/annurev-biochem-060713-035644] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Research into the molecular mechanisms of eukaryotic circadian clocks has proceeded at an electrifying pace. In this review, we discuss advances in our understanding of the structures of central molecular players in the timing oscillators of fungi, insects, and mammals. A series of clock protein structures demonstrate that the PAS (Per/Arnt/Sim) domain has been used with great variation to formulate the transcriptional activators and repressors of the clock. We discuss how posttranslational modifications and external cues, such as light, affect the conformation and function of core clock components. Recent breakthroughs have also revealed novel interactions among clock proteins and new partners that couple the clock to metabolic and developmental pathways. Overall, a picture of clock function has emerged wherein conserved motifs and structural platforms have been elaborated into a highly dynamic collection of interacting molecules that undergo orchestrated changes in chemical structure, conformational state, and partners.
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Affiliation(s)
- Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853;
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26
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Gustafson CL, Partch CL. Emerging models for the molecular basis of mammalian circadian timing. Biochemistry 2014; 54:134-49. [PMID: 25303119 PMCID: PMC4303291 DOI: 10.1021/bi500731f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mammalian circadian timekeeping arises from a transcription-based feedback loop driven by a set of dedicated clock proteins. At its core, the heterodimeric transcription factor CLOCK:BMAL1 activates expression of Period, Cryptochrome, and Rev-Erb genes, which feed back to repress transcription and create oscillations in gene expression that confer circadian timing cues to cellular processes. The formation of different clock protein complexes throughout this transcriptional cycle helps to establish the intrinsic ∼24 h periodicity of the clock; however, current models of circadian timekeeping lack the explanatory power to fully describe this process. Recent studies confirm the presence of at least three distinct regulatory complexes: a transcriptionally active state comprising the CLOCK:BMAL1 heterodimer with its coactivator CBP/p300, an early repressive state containing PER:CRY complexes, and a late repressive state marked by a poised but inactive, DNA-bound CLOCK:BMAL1:CRY1 complex. In this review, we analyze high-resolution structures of core circadian transcriptional regulators and integrate biochemical data to suggest how remodeling of clock protein complexes may be achieved throughout the 24 h cycle. Defining these detailed mechanisms will provide a foundation for understanding the molecular basis of circadian timing and help to establish new platforms for the discovery of therapeutics to manipulate the clock.
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Affiliation(s)
- Chelsea L Gustafson
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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27
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Nangle SN, Rosensweig C, Koike N, Tei H, Takahashi JS, Green CB, Zheng N. Molecular assembly of the period-cryptochrome circadian transcriptional repressor complex. eLife 2014; 3:e03674. [PMID: 25127877 PMCID: PMC4157330 DOI: 10.7554/elife.03674] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/14/2014] [Indexed: 12/20/2022] Open
Abstract
The mammalian circadian clock is driven by a transcriptional-translational feedback loop, which produces robust 24-hr rhythms. Proper oscillation of the clock depends on the complex formation and periodic turnover of the Period and Cryptochrome proteins, which together inhibit their own transcriptional activator complex, CLOCK-BMAL1. We determined the crystal structure of the CRY-binding domain (CBD) of PER2 in complex with CRY2 at 2.8 Å resolution. PER2-CBD adopts a highly extended conformation, embracing CRY2 with a sinuous binding mode. Its N-terminal end tucks into CRY adjacent to a large pocket critical for CLOCK-BMAL1 binding, while its C-terminal half flanks the CRY2 C-terminal helix and sterically hinders the recognition of CRY2 by the FBXL3 ubiquitin ligase. Unexpectedly, a strictly conserved intermolecular zinc finger, whose integrity is important for clock rhythmicity, further stabilizes the complex. Our structure-guided analyses show that these interspersed CRY-interacting regions represent multiple functional modules of PERs at the CRY-binding interface.
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Affiliation(s)
- Shannon N Nangle
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Clark Rosensweig
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hajime Tei
- Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, United States Howard Hughes Medical Institute, University of Washington, Seattle, United States
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Interaction of Circadian Clock Proteins CRY1 and PER2 Is Modulated by Zinc Binding and Disulfide Bond Formation. Cell 2014; 157:1203-15. [DOI: 10.1016/j.cell.2014.03.057] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 02/06/2014] [Accepted: 03/17/2014] [Indexed: 11/22/2022]
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Chun SK, Jang J, Chung S, Yun H, Kim NJ, Jung JW, Son GH, Suh YG, Kim K. Identification and validation of cryptochrome inhibitors that modulate the molecular circadian clock. ACS Chem Biol 2014; 9:703-10. [PMID: 24387302 DOI: 10.1021/cb400752k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Circadian rhythms, biological oscillations with a period of about 24 h, are maintained by a genetically determined innate time-keeping system called the molecular circadian clockwork. Despite the physiological and clinical importance of the circadian clock, the development of small molecule modulators that directly target the core clock machinery has only been recently initiated. In the present study, we aimed to identify novel small molecule modulators influencing the molecular feedback loop of the circadian clock by applying our two-step cell-based screening strategy based on E-box-mediated transcriptional activity to test more than 1000 drug-like compounds. A derivative of 2-ethoxypropanoic acid designated as compound 15 was selected as the most promising candidate in terms of both efficacy and potency. We then performed pull-down assays with the biotinylated compound and find out that both cryptochrome (CRY)1 and 2 (CRY1/2), key negative components of the mammalian circadian clock, as molecular targets of compound 15. In accordance with the binding property, compound 15 enhanced E-box-mediated transcription in a CRY1/2-dependent manner, and more importantly, it attenuated the circadian oscillation of Per2-Luc and Bmal1-dLuc activities in cultured fibroblasts, indicating that compound 15 can functionally inhibit the effects of CRY1/2 in the molecular circadian clockwork. In conclusion, the present study describes the first novel chemical inhibitor of CRY1/2 that inhibits the repressive function of CRY1/2, thereby activating CLOCK-BMAL1-evoked E-box-mediated transcription. Further optimizations and subsequent functional studies of this compound may lead to development of efficient therapeutic strategies for a variety of physiological and metabolic disorders with circadian natures.
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Affiliation(s)
- Sung Kook Chun
- Department
of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Jaebong Jang
- College
of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Sooyoung Chung
- Department
of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Hwayoung Yun
- College
of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Nam-Jung Kim
- Department
of Pharmacy, College of Pharmacy, Kyung Hee University, 26 Kyungheedae-ro,
Dongdaemun-gu, Seoul 130-701, Korea
| | - Jong-Wha Jung
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Korea
| | - Gi Hoon Son
- Department
of Legal Medicine, College of Medicine, Korea University, 73
Inchon-ro, Seongbuk-gu, Seoul 136-705, Korea
| | - Young-Ger Suh
- College
of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Kyungjin Kim
- Department
of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
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Gao P, Yoo SH, Lee KJ, Rosensweig C, Takahashi JS, Chen BP, Green CB. Phosphorylation of the cryptochrome 1 C-terminal tail regulates circadian period length. J Biol Chem 2013; 288:35277-86. [PMID: 24158435 PMCID: PMC3853276 DOI: 10.1074/jbc.m113.509604] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Cryptochrome (CRY) proteins are critical components of the mammalian circadian clock and act to rhythmically repress the activity of the transcriptional activators CLOCK and BMAL1 at the heart of the clock mechanism. The CRY proteins are part of a large repressive complex, the components of which are not completely known. Using mass spectroscopy, we identified the catalytic subunit of DNA-dependent protein kinase as a CRY-interacting protein and found that loss or inhibition of this kinase results in circadian rhythms with abnormally long periods. We then identified serine 588 in the C-terminal tail of mouse CRY1 as a potential DNA-PK phosphorylation site but surprisingly found that the phosphomimetic mutation S588D also results in long period rhythms, similar to the loss of DNA-PK. Consistent with this, we found that phosphorylation of this site is increased in cells lacking DNA-PK, suggesting that DNA-PK negatively regulates the phosphorylation of this site most likely through indirect means. Furthermore, we found that phosphorylation of this site increases the stability of the CRY1 protein and prevents FBXL3-mediated degradation. The phosphorylation of this site is robustly rhythmic in mouse liver nuclei, peaking in the middle of the circadian day at a time when CRY1 levels are declining. Therefore, these data suggest a new role for the C-terminal tail of CRY1 in which phosphorylation rhythmically regulates CRY1 stability and contributes to the proper circadian period length.
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Affiliation(s)
- Peng Gao
- From the Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Seung-Hee Yoo
- From the Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
- the Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, and
| | - Kyung-Jong Lee
- the Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Clark Rosensweig
- From the Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Joseph S. Takahashi
- From the Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
- the Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, and
| | - Benjamin P. Chen
- the Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Carla B. Green
- From the Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
- To whom correspondence should be addressed: Dept. of Neuroscience, ND4.124A, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9111. Tel.: 214-648-7433; Fax: 214-648-1801; E-mail:
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Molecular architecture of the mammalian circadian clock. Trends Cell Biol 2013; 24:90-9. [PMID: 23916625 DOI: 10.1016/j.tcb.2013.07.002] [Citation(s) in RCA: 937] [Impact Index Per Article: 85.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 12/31/2022]
Abstract
Circadian clocks coordinate physiology and behavior with the 24h solar day to provide temporal homeostasis with the external environment. The molecular clocks that drive these intrinsic rhythmic changes are based on interlocked transcription/translation feedback loops that integrate with diverse environmental and metabolic stimuli to generate internal 24h timing. In this review we highlight recent advances in our understanding of the core molecular clock and how it utilizes diverse transcriptional and post-transcriptional mechanisms to impart temporal control onto mammalian physiology. Understanding the way in which biological rhythms are generated throughout the body may provide avenues for temporally directed therapeutics to improve health and prevent disease.
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Czarna A, Berndt A, Singh H, Grudziecki A, Ladurner A, Timinszky G, Kramer A, Wolf E. Structures of Drosophila Cryptochrome and Mouse Cryptochrome1 Provide Insight into Circadian Function. Cell 2013; 153:1394-405. [DOI: 10.1016/j.cell.2013.05.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 02/14/2013] [Accepted: 05/03/2013] [Indexed: 12/28/2022]
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Metz S, Haberzettl K, Frühwirth S, Teich K, Hasewinkel C, Klug G. Interaction of two photoreceptors in the regulation of bacterial photosynthesis genes. Nucleic Acids Res 2012; 40:5901-9. [PMID: 22434878 PMCID: PMC3401432 DOI: 10.1093/nar/gks243] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The expression of photosynthesis genes in the facultatively photosynthetic bacterium Rhodobacter sphaeroides is controlled by the oxygen tension and by light quantity. Two photoreceptor proteins, AppA and CryB, have been identified in the past, which are involved in this regulation. AppA senses light by its N-terminal BLUF domain, its C-terminal part binds heme and is redox-responsive. Through its interaction to the transcriptional repressor PpsR the AppA photoreceptor controls expression of photosynthesis genes. The cryptochrome-like protein CryB was shown to affect regulation of photosynthesis genes, but the underlying signal chain remained unknown. Here we show that CryB interacts with the C-terminal domain of AppA and modulates the binding of AppA to the transcriptional repressor PpsR in a light-dependent manner. Consequently, binding of the transcription factor PpsR to its DNA target is affected by CryB. In agreement with this, all genes of the PpsR regulon showed altered expression levels in a CryB deletion strain after blue-light illumination. These results elucidate for the first time how a bacterial cryptochrome affects gene expression.
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Affiliation(s)
- Sebastian Metz
- Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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