Delayed Cryptochrome Degradation Asymmetrically Alters the Daily Rhythm in Suprachiasmatic Clock Neuron Excitability
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©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling Their Structures
©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2015 Reading Committee: Matthew F. Bush, Chair Robert E. Synovec Dustin J. Maly James E. Bruce Program Authorized to Offer Degree: Chemistry University of Washington Abstract Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni Chair of the Supervisory Committee: Assistant Professor Matthew F. Bush Department of Chemistry Native mass spectrometry (MS) is an increasingly important structural biology technique for characterizing protein complexes. Conventional structural techniques such as X-ray crys- tallography and nuclear magnetic resonance (NMR) spectroscopy can produce very high- resolution structures, however large quantities of protein are needed, heterogeneity com- plicates structural elucidation, and higher-order complexes of biomolecules are difficult to characterize with these techniques. Native MS is rapid and requires very small amounts of sample. Though the data is not as high-resolution, information about stoichiometry, subunit topology, and ligand-binding, is readily obtained, making native MS very complementary to these techniques. When coupled with ion mobility, geometric information in the form of a collision cross section (Ω) can be obtained as well. Integrative modeling approaches are emerging that integrate gas-phase techniques — such as native MS, ion mobility, chemical cross-linking, and other forms of protein MS — with conventional solution-phase techniques and computational modeling. While conducting the research discussed in this dissertation, I used native MS to investigate two biological systems: a mammalian circadian clock protein complex and a series of engineered fusion proteins. -
Transcription Factors of the Core Feedback Loop in the Molecular Circadian Clock Machinery: Internal Timekeeping and Beyond Katalin Csép*
Acta Marisiensis - Seria Medica 2021;67(1):3-11 DOI: 10.2478/amma-2021-0007 REVIEW Transcription factors of the core feedback loop in the molecular circadian clock machinery: internal timekeeping and beyond Katalin Csép* George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, Romania To function more efficiently amid oscillating environmental conditions related to alternating day and night cycles, the circadian clock system developed as an adaptative strategy, serving temporal regulation of internal processes, by anticipating daily recurring changes. At the basis of the circadian clock is a 24-hour oscillation of the expression of clock genes, organized into interconnected self-regulatory transcriptional- translational feedback loops, present throughout the cells of the body, organized into a hierarchical system. Complex combinatorial mecha- nisms of gene expression regulation at pre-transcriptional, transcriptional, post-transcriptional and post-translational level offer stability and flexibility to the system, responsive to the actual conditions. The core clock genes CLOCK/NPAS2, ARNTL1/ARNTL2, PER1/PER2/PER3 and CRY1/CRY2 encode transcription factors responsible for generating the circadian rhythm in the molecular oscillator machinery, but beyond internal timekeeping, additional functions through gene expression regulation and protein interactions provide them key roles in basic mecha- nisms like cell cycle control or metabolism, and orchestration of complex physiological or behavioral processes. Elucidation of these intricate regulatory processes, the role of genetic variations as well as clock desynchronization associated with modern lifestyle, promise important medical implications, from a deeper understanding of etiopathology in rare inherited or common adult disorders, to a better management by the application of chronotherapy. -
Epigenomic and Transcriptional Regulation of Hepatic Metabolism by REV-ERB and Hdac3
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Epigenomic and Transcriptional Regulation of Hepatic Metabolism by REV-ERB and Hdac3 Dan Feng University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Genetics Commons, and the Molecular Biology Commons Recommended Citation Feng, Dan, "Epigenomic and Transcriptional Regulation of Hepatic Metabolism by REV-ERB and Hdac3" (2013). Publicly Accessible Penn Dissertations. 633. https://repository.upenn.edu/edissertations/633 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/633 For more information, please contact [email protected]. Epigenomic and Transcriptional Regulation of Hepatic Metabolism by REV-ERB and Hdac3 Abstract Metabolic activities are regulated by the circadian clock, and disruption of the clock exacerbates metabolic diseases including obesity and diabetes. Transcriptomic studies in metabolic organs suggested that the circadian clock drives the circadian expression of important metabolic genes. Here we show that histone deacetylase 3 (HDAC3) is recruited to the mouse liver genome in a circadian manner. Histone acetylation is inversely related to HDAC3 binding, and this rhythm is lost when HDAC3 is absent. Diurnal recruitment of HDAC3 corresponds to the expression pattern of REV-ERBα, an important component of the circadian clock. REV-ERBα colocalizes with HDAC3 near genes regulating lipid metabolism, and deletion of HDAC3 or Rev-erbα in mouse liver causes hepatic steatosis. Thus, genomic recruitment of HDAC3 by REV-ERBα directs a circadian rhythm of histone acetylation and gene expression required for normal hepatic lipid homeostasis. In addition, we reported that the REV-ERBα paralog, REV- ERBβ also displays circadian binding similar to that of REV-ERBα. -
740464V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/740464; this version posted August 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms Jennifer L. Fribourgh1†, Ashutosh Srivastava2†, Colby R. Sandate3†, Alicia K. Michael1, Peter L. Hsu4, Christin Rakers5, Leslee T. Nguyen1, Megan R. Torgrimson1, Gian Carlo G. Parico1, Sarvind Tripathi1, Ning Zheng4,6, Gabriel C. Lander3, Tsuyoshi Hirota2, Florence Tama2,7,8*, Carrie L. Partch1,9* 1Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 2Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan. 3The Scripps Research Institute, La Jolla, CA 92037, USA. 4Department of Pharmacology, University of Washington, Seattle, WA 98195, USA. 5Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan. 6Howard Hughes Medical Institute, Box 357280, Seattle, WA 98125, USA. 7Department of Physics, Nagoya University, Nagoya 464-8601, Japan. 8RIKEN Center for Computational Science, Kobe 650-0047, Japan. 9Center for Circadian Biology, University of California San Diego, La Jolla, CA 92037, USA. †Equal contributions Correspondence: [email protected] and [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/740464; this version posted August 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Summary Circadian rhythms are generated by a transcription-based feedback loop where CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. -
Qt2vr8f2sg Nosplash 1E9a8a43
Instructions for reviewing your article proof You will need to use Adobe Reader version 7 or above to make comments on this proof, available free from http://get.adobe.com/reader/. Responding to the author query form: Please address each query on the query list, on the proof or in a separate query response list. Editing the proof: Edit the manuscript as necessary, using only the circled tools in the Drawing or Annotation menu. IMPORTANT: All edits must be visible in full on a printed page, or they will be lost in production. Do not use any tool that does not show your changes directly on a printed page. Use Text boxes to add text changes and the drawing tools to indicate insert points or graphics changes. Extensive directions should be addressed in a text box. While most figure edits should be marked on the page, extensive visual changes to figures (e.g., adding scale bars or changes to data) should be accompanied by a new figure file with a written explanation of the changes. Special characters can be inserted into text boxes by pasting from a word processing document or by copying from the list below. α β χ δ ε φ γ η ι ϕ κ λ µ ν ο π θ ρ σ τ υ ϖ ω ξ ψ ζ Α Β Σ Δ Ε Φ Γ Η Ι ϑ Κ Λ Μ Ν Ο Π Θ Ρ Σ Τ Υ ς Ω Ξ Ψ Ζ Å Δ ≥ ≤ ≠ × ± 1° 3ʹ ↑↓ →← RE V IE W The intricate dance of post-translational modifications in the rhythm of life . -
Structural Basis for Dimerization Quality Control
Published as: Nature. 2020 October ; 586(7829): 452–456. HHMI Author ManuscriptHHMI Author Manuscript HHMI Author Manuscript HHMI Author Structural basis for dimerization quality control Elijah L. Mena1, Predrag Jevtić1,2,*, Basil J. Greber3,4,*, Christine L. Gee1,2,*, Brandon G. Lew1,2, David Akopian1, Eva Nogales1,2,3,4, John Kuriyan1,2,3,4,5, Michael Rape1,2,3,# 1Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA 2Howard Hughes Medical Institute, University of California at Berkeley, Berkeley CA 94720, USA 3California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA 4Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5Department of Chemistry, University of California at Berkeley, Berkeley CA 94720, USA Abstract Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration 1. Dimerization quality control (DQC) further improves proteostasis by eliminating complexes of aberrant composition 2, yet how it detects incorrect subunits is still unknown. Here, we provide structural insight into target selection by SCFFBXL17, a DQC E3 ligase that ubiquitylates and helps degrade inactive heterodimers of BTB proteins, while sparing functional homodimers. We find that SCFFBXL17 disrupts aberrant BTB dimers that fail to stabilize an intermolecular β-sheet around a highly divergent β-strand of the BTB domain. Complex dissociation allows SCFFBXL17 to wrap around a single BTB domain for robust ubiquitylation. SCFFBXL17 therefore probes both shape and complementarity of BTB domains, a mechanism that is well suited to establish quality control of complex composition for recurrent interaction modules. -
Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm
Competing E3 Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm Seung-Hee Yoo,1,2 Jennifer A. Mohawk,1,2,7 Sandra M. Siepka,4,7 Yongli Shan,1 Seong Kwon Huh,1 Hee-Kyung Hong,4 Izabela Kornblum,2 Vivek Kumar,1,2 Nobuya Koike,1 Ming Xu,3 Justin Nussbaum,5 Xinran Liu,1,8 Zheng Chen,6 Zhijian J. Chen,2,3 Carla B. Green,1,5 and Joseph S. Takahashi1,2,* 1Department of Neuroscience 2Howard Hughes Medical Institute 3Department of Molecular Biology University of Texas Southwestern Medical Center, Dallas, TX 75390, USA 4Department of Neurobiology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA 5Department of Biology, University of Virginia, Charlottesville, VA 22904, USA 6Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA 7These authors contributed equally to this work 8Present address: Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.cell.2013.01.055 SUMMARY and repress the activity of CLOCK:BMAL1 to inhibit their own transcription (King et al., 1997; Gekakis et al., 1998; Lee et al., Period determination in the mammalian circadian 2001). Bmal1 expression is also regulated by a secondary feed- clock involves the turnover rate of the repressors back loop comprised of the nuclear hormone receptors REV- CRY and PER. We show that CRY ubiquitination ERBa/b and the retinoid-related orphan receptors (Preitner engages two competing E3 ligase complexes that et al., 2002; Cho et al., 2012). -
The Complex Interplay Between MYC and the Molecular Circadian Clock in Cancer
International Journal of Molecular Sciences Review MYC Ran Up the Clock: The Complex Interplay between MYC and the Molecular Circadian Clock in Cancer Jamison B. Burchett 1, Amelia M. Knudsen-Clark 2 and Brian J. Altman 1,3,* 1 Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA; [email protected] 2 Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; [email protected] 3 Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA * Correspondence: [email protected] Abstract: The MYC oncoprotein and its family members N-MYC and L-MYC are known to drive a wide variety of human cancers. Emerging evidence suggests that MYC has a bi-directional relationship with the molecular clock in cancer. The molecular clock is responsible for circadian (~24 h) rhythms in most eukaryotic cells and organisms, as a mechanism to adapt to light/dark cycles. Disruption of human circadian rhythms, such as through shift work, may serve as a risk factor for cancer, but connections with oncogenic drivers such as MYC were previously not well understood. In this review, we examine recent evidence that MYC in cancer cells can disrupt the molecular clock; and conversely, that molecular clock disruption in cancer can deregulate and elevate MYC. Since MYC and the molecular clock control many of the same processes, we then consider competition between MYC and the molecular clock in several select aspects of tumor biology, including chromatin state, global transcriptional profile, metabolic rewiring, and immune infiltrate in the tumor. -
Epigenetic Regulation of Circadian Rhythm and Its Possible Role in Diabetes Mellitus
International Journal of Molecular Sciences Review Epigenetic Regulation of Circadian Rhythm and Its Possible Role in Diabetes Mellitus Michael Hudec 1,*, Pavlina Dankova 2, Roman Solc 2 , Nardjas Bettazova 1 and Marie Cerna 1 1 Department of Medical Genetics, Third Faculty of Medicine, Charles University; Ruská 87, 100 00 Prague, Czech Republic; [email protected] (N.B.); [email protected] (M.C.) 2 Department of Anthropology and Human Genetics, Faculty of Science, Charles University; Viniˇcná 7, 128 00 Prague, Czech Republic; [email protected] (P.D.); [email protected] (R.S.) * Correspondence: [email protected]; Tel.: +420-737242493 Received: 24 January 2020; Accepted: 21 April 2020; Published: 24 April 2020 Abstract: This review aims to summarize the knowledge about the relationship between circadian rhythms and their influence on the development of type 2 diabetes mellitus (T2DM) and metabolic syndrome. Circadian rhythms are controlled by internal molecular feedback loops that synchronize the organism with the external environment. These loops are affected by genetic and epigenetic factors. Genetic factors include polymorphisms and mutations of circadian genes. The expression of circadian genes is regulated by epigenetic mechanisms that change from prenatal development to old age. Epigenetic modifications are influenced by the external environment. Most of these modifications are affected by our own life style. Irregular circadian rhythm and low quality of sleep have been shown to increase the risk of developing T2DM and other metabolic disorders. Here, we attempt to provide a wide description of mutual relationships between epigenetic regulation, circadian rhythm, aging process and highlight new evidences that show possible therapeutic advance in the field of chrono-medicine which will be more important in the upcoming years. -
Ubiquitin Ligase Siah2 Regulates Reverbα Degradation and the Mammalian Circadian Clock
Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock Jason P. DeBruynea,1, Julie E. Baggsa, Trey K. Satob,2, and John B. Hogeneschb,1 aNeuroscience Institute, Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA 30310; and bDepartment of Pharmacology, Penn Genome Frontiers Institute, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA, 19104 Edited* by Joseph S. Takahashi, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, and approved August 19, 2015 (received for review January 22, 2015) Regulated degradation of proteins by the proteasome is often In many cases, ubiquitin ligases for proteins have been re- critical to their function in dynamic cellular pathways. The molecular covered from random mutagenesis screens for genes that regu- clock underlying mammalian circadian rhythms relies on the rhythmic late a global biological process such as cell division. These screens expression and degradation of its core components. However, usually are designed to identify genes involved in complex bi- because the tools available for identifying the mechanisms un- ological processes rather than a specific biochemical event such derlying the degradation of a specific protein are limited, the as the degradation of a particular protein. Protein interaction mechanisms regulating clock protein degradation are only begin- screening has been applied to identify E3 ligase–substrate in- ning to be elucidated. Here we describe a cell-based functional teractions (reviewed in ref. 12). However, this approach is most screening approach designed to quickly identify the ubiquitin E3 applicable when the E3 ligase–substrate interactions are strong ligases that induce the degradation of potentially any protein of and stable and may not work for transient enzyme–substrate interest. -
Early Doors (Edo) Mutant Mouse Reveals the Importance of Period 2 (PER2) PAS Domain Structure for Circadian Pacemaking
Early doors (Edo) mutant mouse reveals the importance of period 2 (PER2) PAS domain structure for circadian pacemaking Stefania Militia,1, Elizabeth S. Maywoodb,1, Colby R. Sandatec, Johanna E. Cheshamb, Alun R. Barnarda,2, Michael J. Parsonsa, Jennifer L. Viberta, Greg M. Joynsona, Carrie L. Partchc, Michael H. Hastingsb, and Patrick M. Nolana,3 aMedical Research Council Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom; bDivision of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom; and cDepartment of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064 Edited by Joseph S. Takahashi, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, and approved January 26, 2016 (received for review September 2, 2015) The suprachiasmatic nucleus (SCN) defines 24 h of time via a kinase 1e (Csnk1e) (14) is a hypermorph that accelerates the clock transcriptional/posttranslational feedback loop in which trans- of rodents (15). Thus, phosphorylation, PER protein stability, and activation of Per (period) and Cry (cryptochrome) genes by BMAL1– circadian period are intimately linked (16). CLOCK complexes is suppressed by PER–CRY complexes. The Current knowledge of the structural basis of circadian tran- molecular/structural basis of how circadian protein complexes scription and its repression is limited, but it is becoming clear function is poorly understood. We describe a novel N-ethyl-N-nitro- that modular PAS domains form protein interactions that are sourea (ENU)-induced mutation, early doors (Edo), in the PER-ARNT- important for progression of the circadian TTFL. The crystal SIM (PAS) domain dimerization region of period 2 (PER2) (I324N) structures of mouse CLOCK and BMAL1 have revealed how that accelerates the circadian clock of Per2Edo/Edo mice by 1.5 h. -
Nangle Et Al. 2014 1 1 2 3 4 5 6 Molecular Assembly of the Period-Cryptochrome Circadian Transcriptional Repressor Complex 7
Nangle et al. 2014 1 2 3 4 5 6 7 Molecular Assembly of the Period-Cryptochrome Circadian Transcriptional Repressor Complex 8 9 Shannon N. Nangle1, ‡, Clark Rosensweig3, ‡, Nobuya Koike5, Hajime Tei6, Joseph S. Takahashi3,4,*, Carla B. 10 Green3,* & Ning Zheng1,2,* 11 12 13 14 15 1Department of Pharmacology and 2Howard Hughes Medical Institute, Box 357280, University of Washington, 16 Seattle, WA 98195, USA 17 3Department of Neuroscience and 4Howard Hughes Medical Institute, The University of Texas Southwestern 18 Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA 19 5Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine 20 Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, Japan 21 6Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan 22 23 ‡ These authors contributed equally to this work. 24 *Correspondence: [email protected], [email protected], [email protected] 25 26 1 Nangle et al. 2014 27 ABSTRACT 28 The mammalian circadian clock is driven by a transcriptional-translational feedback loop, which produces 29 robust 24-hr rhythms. Proper oscillation of the clock depends on the complex formation and cyclic turnover of 30 the Period and Cryptochrome proteins, which together inhibit their own transcriptional activator complex, 31 CLOCK-BMAL1. We determined the crystal structure of the CRY-binding domain (CBD) of PER2 in complex 32 with CRY2 at 2.8 Å resolution. PER2-CBD adopts a highly extended conformation, embracing CRY2 with a 33 sinuous binding mode. Its N-terminal end tucks into CRY adjacent to a large pocket critical for CLOCK- 34 BMAL1 binding, while its C-terminal half flanks the CRY2 C-terminal helix and sterically hinders the 35 recognition of CRY2 by the FBXL3 ubiquitin ligase.