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Kalmer TL, Ancajas CMF, Cohen CI, McDaniel JM, Oyedele AS, Thirman HL, Walker AS. Statistical Coupling Analysis Predicts Correlated Motions in Dihydrofolate Reductase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599103. [PMID: 38948820 PMCID: PMC11213021 DOI: 10.1101/2024.06.18.599103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The role of dynamics in enzymatic function is a highly debated topic. Dihydrofolate reductase (DHFR), due to its universality and the depth with which it has been studied, is a model system in this debate. Myriad previous works have identified networks of residues in positions near to and remote from the active site that are involved in dynamics and others that are important for catalysis. For example, specific mutations on the Met20 loop in E. coli DHFR (N23PP/S148A) are known to disrupt millisecond-timescale motions and reduce catalytic activity. However, how and if networks of dynamically coupled residues influence the evolution of DHFR is still an unanswered question. In this study, we first identify, by statistical coupling analysis and molecular dynamic simulations, a network of coevolving residues, which possess increased correlated motions. We then go on to show that allosteric communication in this network is selectively knocked down in N23PP/S148A mutant E. coli DHFR. Finally, we identify two sites in the human DHFR sector which may accommodate the Met20 loop double proline mutation while preserving dynamics. These findings strongly implicate protein dynamics as a driving force for evolution.
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Affiliation(s)
- Thomas L. Kalmer
- Department of Chemistry, Vanderbilt University Nashville, TN, USA
| | | | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jade M. McDaniel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Hannah L. Thirman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN, USA
| | - Allison S. Walker
- Department of Chemistry, Vanderbilt University Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
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2
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Parlak GC, Baris I, Gul S, Kavakli IH. Functional characterization of the CRY2 circadian clock component variant p.Ser420Phe revealed a new degradation pathway for CRY2. J Biol Chem 2023; 299:105451. [PMID: 37951306 PMCID: PMC10731238 DOI: 10.1016/j.jbc.2023.105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/13/2023] Open
Abstract
Cryptochromes (CRYs) are essential components of the circadian clock, playing a pivotal role as transcriptional repressors. Despite their significance, the precise mechanisms underlying CRYs' involvement in the circadian clock remain incompletely understood. In this study, we identified a rare CRY2 variant, p.Ser420Phe, from the 1000 Genomes Project and Ensembl database that is located in the functionally important coiled-coil-like helix (CC-helix) region. Functional characterization of this variant at the cellular level revealed that p.Ser420Phe CRY2 had reduced repression activity on CLOCK:BMAL1-driven transcription due to its reduced affinity to the core clock protein PER2 and defective translocation into the nucleus. Intriguingly, the CRY2 variant exhibited an unexpected resistance to degradation via the canonical proteasomal pathway, primarily due to the loss of interactions with E3 ligases (FBXL3 and FBXL21), which suggests Ser-420 of CRY2 is required for the interaction with E3 ligases. Further studies revealed that wild-type and CRY2 variants are degraded by the lysosomal-mediated degradation pathway, a mechanism not previously associated with CRY2. Surprisingly, our complementation study with Cry1-/-Cry2-/- double knockout mouse embryonic fibroblast cells indicated that the CRY2 variant caused a 7 h shorter circadian period length in contrast to the observed prolonged period length in CRY2-/- cell lines. In summary, this study reveals a hitherto unknown degradation pathway for CRY2, shedding new light on the regulation of circadian rhythm period length.
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Affiliation(s)
- Gizem Cagla Parlak
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkiye
| | - Ibrahim Baris
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkiye
| | - Seref Gul
- Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Turkiye
| | - Ibrahim Halil Kavakli
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkiye; Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkiye.
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3
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Hosokawa Y, Morita H, Nakamura M, Yamamoto J. A deazariboflavin chromophore kinetically stabilizes reduced FAD state in a bifunctional cryptochrome. Sci Rep 2023; 13:16682. [PMID: 37794070 PMCID: PMC10551024 DOI: 10.1038/s41598-023-43930-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023] Open
Abstract
An animal-like cryptochrome derived from Chlamydomonas reinhardtii (CraCRY) is a bifunctional flavoenzyme harboring flavin adenine dinucleotide (FAD) as a photoreceptive/catalytic center and functions both in the regulation of gene transcription and the repair of UV-induced DNA lesions in a light-dependent manner, using different FAD redox states. To address how CraCRY stabilizes the physiologically relevant redox state of FAD, we investigated the thermodynamic and kinetic stability of the two-electron reduced anionic FAD state (FADH-) in CraCRY and related (6-4) photolyases. The thermodynamic stability of FADH- remained almost the same compared to that of all tested proteins. However, the kinetic stability of FADH- varied remarkably depending on the local structure of the secondary pocket, where an auxiliary chromophore, 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF), can be accommodated. The observed effect of 8-HDF uptake on the enhancement of the kinetic stability of FADH- suggests an essential role of 8-HDF in the bifunctionality of CraCRY.
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Affiliation(s)
- Yuhei Hosokawa
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Hiroyoshi Morita
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Mai Nakamura
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.
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4
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Laothamatas I, Rasmussen ES, Green CB, Takahashi JS. Metabolic and chemical architecture of the mammalian circadian clock. Cell Chem Biol 2023; 30:1033-1052. [PMID: 37708890 PMCID: PMC10631358 DOI: 10.1016/j.chembiol.2023.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Circadian rhythms are endogenous periodic biological processes that occur on a daily timescale. These rhythms are generated by a transcriptional/translational feedback loop that consists of the CLOCK-BMAL1 heterodimeric transcriptional activator complex and the PER1/2-CRY1/2-CK1δ/ε repressive complex. The output pathways of this molecular feedback loop generate circadian rhythmicity in various biological processes. Among these, metabolism is a primary regulatory target of the circadian clock which can also feedback to modulate clock function. This intertwined relationship between circadian rhythms and metabolism makes circadian clock components promising therapeutic targets. Despite this, pharmacological therapeutics that target the circadian clock are relatively rare. In this review, we hope to stimulate interest in chemical chronobiology by providing a comprehensive background on the molecular mechanism of mammalian circadian rhythms and their connection to metabolism, highlighting important studies in the chemical approach to circadian research, and offering our perspectives on future developments in the field.
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Affiliation(s)
- Isara Laothamatas
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Emil Sjulstok Rasmussen
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, 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.
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5
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Lin C, Feng S, DeOliveira CC, Crane BR. Cryptochrome-Timeless structure reveals circadian clock timing mechanisms. Nature 2023; 617:194-199. [PMID: 37100907 PMCID: PMC11034853 DOI: 10.1038/s41586-023-06009-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/23/2023] [Indexed: 04/28/2023]
Abstract
Circadian rhythms influence many behaviours and diseases1,2. They arise from oscillations in gene expression caused by repressor proteins that directly inhibit transcription of their own genes. The fly circadian clock offers a valuable model for studying these processes, wherein Timeless (Tim) plays a critical role in mediating nuclear entry of the transcriptional repressor Period (Per) and the photoreceptor Cryptochrome (Cry) entrains the clock by triggering Tim degradation in light2,3. Here, through cryogenic electron microscopy of the Cry-Tim complex, we show how a light-sensing cryptochrome recognizes its target. Cry engages a continuous core of amino-terminal Tim armadillo repeats, resembling how photolyases recognize damaged DNA, and binds a C-terminal Tim helix, reminiscent of the interactions between light-insensitive cryptochromes and their partners in mammals. The structure highlights how the Cry flavin cofactor undergoes conformational changes that couple to large-scale rearrangements at the molecular interface, and how a phosphorylated segment in Tim may impact clock period by regulating the binding of Importin-α and the nuclear import of Tim-Per4,5. Moreover, the structure reveals that the N terminus of Tim inserts into the restructured Cry pocket to replace the autoinhibitory C-terminal tail released by light, thereby providing a possible explanation for how the long-short Tim polymorphism adapts flies to different climates6,7.
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Affiliation(s)
- Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Shi Feng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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6
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Foroutannejad S, Good LL, Lin C, Carter ZI, Tadesse MG, Lucius AL, Crane BR, Maillard RA. The cofactor-dependent folding mechanism of Drosophila cryptochrome revealed by single-molecule pulling experiments. Nat Commun 2023; 14:1057. [PMID: 36828841 PMCID: PMC9958137 DOI: 10.1038/s41467-023-36701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
The link between cofactor binding and protein activity is well-established. However, how cofactor interactions modulate folding of large proteins remains unknown. We use optical tweezers, clustering and global fitting to dissect the folding mechanism of Drosophila cryptochrome (dCRY), a 542-residue protein that binds FAD, one of the most chemically and structurally complex cofactors in nature. We show that the first dCRY parts to fold are independent of FAD, but later steps are FAD-driven as the remaining polypeptide folds around the cofactor. FAD binds to largely unfolded intermediates, yet with association kinetics above the diffusion-limit. Interestingly, not all FAD moieties are required for folding: whereas the isoalloxazine ring linked to ribitol and one phosphate is sufficient to drive complete folding, the adenosine ring with phosphates only leads to partial folding. Lastly, we propose a dCRY folding model where regions that undergo conformational transitions during signal transduction are the last to fold.
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Affiliation(s)
| | - Lydia L Good
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Changfan Lin
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zachariah I Carter
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mahlet G Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brian R Crane
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
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7
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Endogenous circadian reporters reveal functional differences of PERIOD paralogs and the significance of PERIOD:CK1 stable interaction. Proc Natl Acad Sci U S A 2023; 120:e2212255120. [PMID: 36724252 PMCID: PMC9962996 DOI: 10.1073/pnas.2212255120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Adverse consequences from having a faulty circadian clock include compromised sleep quality and poor performance in the short-term, and metabolic diseases and cancer in the long-term. However, our understanding of circadian disorders is limited by the incompleteness of our molecular models and our dearth of defined mutant models. Because it would be prohibitively expensive to develop live animal models to study the full range of complicated clock mechanisms, we developed PER1-luc and PER2-luc endogenous circadian reporters in a validated clock cell model, U-2 OS, where the genome can be easily manipulated, and functional consequences of mutations can be accurately studied. When major clock genes were knocked out in these cells, circadian rhythms were modulated similarly compared with corresponding mutant mice, validating the platform for genetics studies. Using these reporter cells, we uncovered critical differences between two paralogs of PER. Although PER1 and PER2 are considered redundant and either one can serve as a pacemaker alone, they were dramatically different in biochemical parameters such as stability and phosphorylation kinetics. Consistently, circadian phase was dramatically different between PER1 and PER2 knockout reporter cells. We further showed that the stable binding of casein kinase1δ/ε to PER is not required for PER phosphorylation itself, but is critical for delayed timing of phosphorylation. Our system can be used as an efficient platform to study circadian disorders associated with pathogenic mutations and their underlying molecular mechanisms.
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8
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Oliva F, Musiani F, Giorgetti A, De Rubeis S, Sorokina O, Armstrong DJ, Carloni P, Ruggerone P. Modelling eNvironment for Isoforms (MoNvIso): A general platform to predict structural determinants of protein isoforms in genetic diseases. Front Chem 2023; 10:1059593. [PMID: 36700074 PMCID: PMC9868658 DOI: 10.3389/fchem.2022.1059593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/06/2022] [Indexed: 01/11/2023] Open
Abstract
The seamless integration of human disease-related mutation data into protein structures is an essential component of any attempt to correctly assess the impact of the mutation. The key step preliminary to any structural modelling is the identification of the isoforms onto which mutations should be mapped due to there being several functionally different protein isoforms from the same gene. To handle large sets of data coming from omics techniques, this challenging task needs to be automatized. Here we present the MoNvIso (Modelling eNvironment for Isoforms) code, which identifies the most useful isoform for computational modelling, balancing the coverage of mutations of interest and the availability of templates to build a structural model of both the wild-type isoform and the related variants.
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Affiliation(s)
- Francesco Oliva
- Department of Physics, University of Cagliari, Monserrato (CA), Italy,Institute of Neuroscience and Medicine INM-9, Institute for Advanced Simulations IAS-5, Forschungszentrum Jülich, Jülich, Germany
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alejandro Giorgetti
- Institute of Neuroscience and Medicine INM-9, Institute for Advanced Simulations IAS-5, Forschungszentrum Jülich, Jülich, Germany,Department of Biotechnology, University of Verona, Verona, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Oksana Sorokina
- The School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas J. Armstrong
- Institute of Neuroscience and Medicine INM-9, Institute for Advanced Simulations IAS-5, Forschungszentrum Jülich, Jülich, Germany,The School of Informatics, University of Edinburgh, Edinburgh, United Kingdom,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Paolo Carloni
- Institute of Neuroscience and Medicine INM-9, Institute for Advanced Simulations IAS-5, Forschungszentrum Jülich, Jülich, Germany,Department of Physics, RWTH Aachen University, Aachen, Germany,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato (CA), Italy,*Correspondence: Paolo Ruggerone,
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9
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Calloni G, Vabulas RM. The structural and functional roles of the flavin cofactor FAD in mammalian cryptochromes. Front Mol Biosci 2023; 9:1081661. [PMID: 36660433 PMCID: PMC9845712 DOI: 10.3389/fmolb.2022.1081661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
The importance of circadian rhythms in human health and disease calls for a thorough understanding of the underlying molecular machinery, including its key components, the flavin adenine dinucleotide (FAD)-containing flavoproteins cryptochrome 1 and 2. Contrary to their Drosophila counterparts, mammalian cryptochromes are direct suppressors of circadian transcription and act independently of light. Light-independence poses the question regarding the role of the cofactor FAD in mammalian cryptochromes. The weak binding of the cofactor in vitro argues against its relevance and might be a functionless evolutionary remnant. From the other side, the FAD-binding pocket constitutes the part of mammalian cryptochromes directly related to their ubiquitylation by the ubiquitin ligase Fbxl3 and is the target for protein-stabilizing small molecules. Increased supplies of FAD stabilize cryptochromes in cell culture, and the depletion of the FAD precursor riboflavin with simultaneous knock-down of riboflavin kinase affects the expression of circadian genes in mice. This review presents the classical and more recent studies in the field, which help to comprehend the role of FAD for the stability and function of mammalian cryptochromes.
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Affiliation(s)
| | - R. Martin Vabulas
- Institute of Biochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany,*Correspondence: R. Martin Vabulas,
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10
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Zhang Z, Han T, Sui J, Wang H. Cryptochrome-mediated blue-light signal contributes to carotenoids biosynthesis in microalgae. Front Microbiol 2022; 13:1083387. [PMID: 36620041 PMCID: PMC9813510 DOI: 10.3389/fmicb.2022.1083387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Microalgae are considered as ideal cell factories for producing natural carotenoids which display favorable biological activities. As the most important abiotic factor, light not only provides energy for photosynthetic metabolism, but also regulates numerous biological processes. Blue light is the main wavelength of light that can travel through water. Previous studies have shown that blue light triggered carotenoid accumulation in several microalgae species, but the molecular mechanism remains unclear. Cryptochromes were blue-light-absorbing photoreceptors that have been found in all studied algal genomes. In this study, several different types of cryptochrome genes were cloned from Haematococcus pluvialis and Phaeodactylum tricornutum. Among them, cryptochrome genes HpCRY4 from H. pluvialis and PtCPF1 from P. tricornutum were upregulated under blue light treatment, in correlation with the increase of astaxanthin and fucoxanthin contents. Besides, heterologous expression and gene knockout was performed to verify the function of HpCRY4 and PtCPF1 in regulating carotenoid biosynthesis in microalgae. These results indicate that carotenoid biosynthesis in microalgae promoted by blue light was mediated by cryptochromes as photoreceptors.
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Affiliation(s)
- Zhongyi Zhang
- Solar Energy Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao, China
| | - Tianli Han
- Solar Energy Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao, China
| | - Jikang Sui
- Solar Energy Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao, China
| | - Hui Wang
- Solar Energy Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao, China,Shandong Energy Research Institute, Qingdao, China,*Correspondence: Hui Wang,
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11
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Yagi M, Miller S, Nagai Y, Inuki S, Sato A, Hirota T. A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins. F1000Res 2022; 11:1016. [PMID: 36226040 PMCID: PMC9523283 DOI: 10.12688/f1000research.124658.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Impairment of the circadian clock has been associated with numerous diseases, including sleep disorders and metabolic disease. Although small molecules that modulate clock function may form the basis of drug discovery of clock-related diseases, only a few compounds that selectively target core clock proteins have been identified. Three scaffolds were previously discovered as small-molecule activators of the clock protein Cryptochrome (CRY), and they have been providing powerful tools to understand and control the circadian clock system. Identifying new scaffolds will expand the possibilities of drug discovery. Methods: A methylbenzimidazole derivative TH401 identified from cell-based circadian screens was characterized. Effects of TH401 on circadian rhythms were evaluated in cellular assays. Functional assays and X-ray crystallography were used to elucidate the effects of the compound on CRY1 and CRY2 isoforms. Results: TH401 lengthened the period of circadian rhythms and stabilized both CRY1 and CRY2. The compound repressed Per2 reporter activity, which was reduced by Cry1 or Cry2 knockout and abolished by Cry1/Cry2 double knockout, indicating the dependence on CRY isoforms. Thermal shift assays showed slightly higher interaction of TH401 with CRY2 over CRY1. The crystal structure of CRY1 in complex with TH401 revealed a conformational change of the gatekeeper W399, which is involved in isoform-selectivity determination. Conclusions: The present study identified a new small molecule TH401 that targets both CRY isoforms. This compound has expanded the chemical diversity of CRY activators, and will ultimately aid in the development of therapeutics against circadian clock-related disorders.
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Affiliation(s)
- Moeri Yagi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan
| | - Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan,
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12
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CRY2 isoform selectivity of a circadian clock modulator with antiglioblastoma efficacy. Proc Natl Acad Sci U S A 2022; 119:e2203936119. [PMID: 36161947 PMCID: PMC9546630 DOI: 10.1073/pnas.2203936119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mammalian cryptochrome isoforms, CRY1 and CRY2, are core circadian clock regulators that work redundantly. Recent studies revealed distinct roles of these closely related homologs in clock output pathways. Isoform-selective control of CRY1 and CRY2 is critical for further understanding their redundant and distinct roles. KL001 was the first identified small-molecule CRY modulator that activates both CRY1 and CRY2. SHP656 is an orally available KL001 derivative and has shown efficacy in blood glucose control and inhibition of glioblastoma stem cell (GSC) growth in animal models. However, CRY isoform selectivity of SHP656 was uncharacterized, limiting understanding of the roles of CRY1 and CRY2. Here, we report the elucidation of CRY2 selectivity of SHP656. SHP656 lengthened cellular circadian period in a CRY2-dependent manner and selectively interacted with CRY2. By determining the X-ray crystal structure of CRY2 in complex with SHP656 and performing molecular dynamics simulations, we elucidated compound interaction mechanisms. SHP656 binding was compatible with the intrinsic CRY2 gatekeeper W417 "in" orientation and also a close "further in" conformation. Perturbation of W417 interaction with the lid loop resulted in a reduced effect of SHP656 on CRY2, supporting an important role of gatekeeper orientation in isoform selectivity. We also identified the R form of SHP656 (called SHP1703) as the active isomer. Treatment with SHP1703 effectively reduced GSC viability. Our results suggest a direct role of CRY2 in glioblastoma antitumorigenesis and provide a rationale for the selective modulation of CRY isoforms in the therapeutic treatment of glioblastoma and other circadian clock-related diseases.
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13
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Deppisch P, Helfrich-Förster C, Senthilan PR. The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution. Genes (Basel) 2022; 13:genes13091613. [PMID: 36140781 PMCID: PMC9498864 DOI: 10.3390/genes13091613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.
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14
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Rasmussen ES, Takahashi JS, Green CB. Time to target the circadian clock for drug discovery. Trends Biochem Sci 2022; 47:745-758. [PMID: 35577675 PMCID: PMC9378619 DOI: 10.1016/j.tibs.2022.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
The circadian clock is an intracellular timekeeping device that drives daily rhythms in diverse and extensive processes throughout the body. The clock mechanism comprises a core transcription/translation negative feedback loop that is modulated by a complex set of additional interlocking feedback loops. Pharmacological manipulation of the clock may be valuable for treating many maladies including jet lag, shift work and related sleep disorders, various metabolic diseases, and cancer. We review recent identification of small-molecule clock modulators and discuss the biochemical features of the core clock that may be amenable to future drug discovery.
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Affiliation(s)
- Emil Sjulstok Rasmussen
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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15
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Parlak GC, Camur BB, Gul S, Ozcan O, Baris I, Kavakli IH. The secondary pocket of Cryptochrome 2 is important for the regulation of its stability and localization. J Biol Chem 2022; 298:102334. [PMID: 35933018 PMCID: PMC9442382 DOI: 10.1016/j.jbc.2022.102334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/28/2022] Open
Abstract
Human clock-gene variations contribute to the phenotypic differences observed in various behavioral and physiological processes such as diurnal preference, sleep, metabolism, mood regulation, addiction, and fertility. However, little is known about the possible effects of identified variations at the molecular level. In this study, we performed a functional characterization at the cellular level of rare CRYPTOCHROME 2 (CRY2) missense variations that were identified from the Ensembl database. Our structural studies revealed that three variations (p.Pro123Leu, p.Asp406His, p.Ser410Ile) are located at the rim of the secondary pocket of CRY2. We show these variants were unable to repress CLOCK/BMAL1-driven transcription in a cell-based reporter assay and had reduced affinity to CLOCK/BMAL1. Furthermore, our biochemical studies indicated that the variants were less stable than the wild-type CRY2, which could be rescued in the presence of Period 2 (PER2), another core clock protein. Finally, we found these variants were unable to properly localize to the nucleus, and thereby were unable to rescue the circadian rhythm in a Cry1-/-Cry2-/- double-knockout mouse embryonic fibroblast cell line. Collectively, our data suggest that the rim of the secondary pocket of CRY2 plays a significant role in its nuclear localization independently of PER2 and in the intact circadian rhythm at the cellular level.
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Affiliation(s)
- Gizem Cagla Parlak
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Bilge Bahar Camur
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Seref Gul
- Istanbul University, Department of Biology, Biotechnology Division, 34134 Suleymaniye, Istanbul, Turkey
| | - Onur Ozcan
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Ibrahim Baris
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey; Koc university Department Chemical and Biological Engineering, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey.
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16
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Taleb Z, Karpowicz P. Circadian regulation of digestive and metabolic tissues. Am J Physiol Cell Physiol 2022; 323:C306-C321. [PMID: 35675638 DOI: 10.1152/ajpcell.00166.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The circadian clock is a self-sustained molecular timekeeper that drives 24-h (circadian) rhythms in animals. The clock governs important aspects of behavior and physiology including wake/sleep activity cycles that regulate the activity of metabolic and digestive systems. Light/dark cycles (photoperiod) and cycles in the time of feeding synchronize the circadian clock to the surrounding environment, providing an anticipatory benefit that promotes digestive health. The availability of animal models targeting the genetic components of the circadian clock has made it possible to investigate the circadian clock's role in cellular functions. Circadian clock genes have been shown to regulate the physiological function of hepatocytes, gastrointestinal cells, and adipocytes; disruption of the circadian clock leads to the exacerbation of liver diseases and liver cancer, inflammatory bowel disease and colorectal cancer, and obesity. Previous findings provide strong evidence that the circadian clock plays an integral role in digestive/metabolic disease pathogenesis, hence, the circadian clock is a necessary component in metabolic and digestive health and homeostasis. Circadian rhythms and circadian clock function provide an opportunity to improve the prevention and treatment of digestive and metabolic diseases by aligning digestive system tissue with the 24-h day.
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Affiliation(s)
- Zainab Taleb
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
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17
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Protein interaction networks of the mammalian core clock proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:207-233. [PMID: 35871891 DOI: 10.1016/bs.apcsb.2022.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Circadian rhythm is a 24-h cycle that regulates the biochemical and behavioral changes of organisms. It controls a wide range of functions, from gene expression to behavior, allowing organisms to anticipate daily changes in their environment. In mammals, circadian rhythm is generated by a complex transcriptional and translational feedback loop mechanism. The binding of CLOCK/BMAL1 heterodimer to the E-box of DNA located within the promoter region initiates transcription of clock control genes including the transcription of the other two core clock genes of Periods (Pers) and Cryptochromes (Crys). Then PERs and CRYs along with casein kinase 1ɛ/Δ translocate into the nucleus where they suppress CLOCK/BMAL1 transactivation and, in turn, clock-regulated gene expression. Various clock components must be operational to aid in their stabilization and period extension in circadian rhythm. In this review, we have highlighted the recent progress for the core clock interacting proteins to maintain and to stabilize circadian rhythm in mammals.
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18
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Vicedomini R, Bouly JP, Laine E, Falciatore A, Carbone A. Multiple profile models extract features from protein sequence data and resolve functional diversity of very different protein families. Mol Biol Evol 2022; 39:6556147. [PMID: 35353898 PMCID: PMC9016551 DOI: 10.1093/molbev/msac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Functional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyse sequences with multiple profile models combined together. ProfileView classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups. We validate ProfileView on seven classes of widespread proteins involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. Profile-View agrees with the large set of functional data collected for these proteins from the literature regarding the organisation into functional subgroups and residues that characterise the functions. In addition, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of novel biological functions. On protein families with complex domain architecture, ProfileView functional classification reconciles domain combinations, unlike phylogenetic reconstruction. ProfileView proves to outperform the functional classification approach PANTHER, the two k-mer based methods CUPP and eCAMI and a neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.
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Affiliation(s)
- R Vicedomini
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,Sorbonne Université, Institut des Sciences du Calcul et des Données
| | - J P Bouly
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,CNRS, Sorbonne Université Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae - UMR7141, Paris, France
| | - E Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France
| | - A Falciatore
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,CNRS, Sorbonne Université Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae - UMR7141, Paris, France
| | - A Carbone
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,Institut Universitaire de France, Paris 75005, France
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19
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Identification of novel small molecules targeting core clock proteins to regulate circadian rhythm. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2021.100730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Miller S, Hirota T. Structural and Chemical Biology Approaches Reveal Isoform-Selective Mechanisms of Ligand Interactions in Mammalian Cryptochromes. Front Physiol 2022; 13:837280. [PMID: 35153842 PMCID: PMC8831909 DOI: 10.3389/fphys.2022.837280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/05/2022] [Indexed: 01/27/2023] Open
Abstract
Cryptochromes (CRYs) are core components of the circadian feedback loop in mammals, which regulates circadian rhythmicity in a variety of physiological processes including sleep–wake cycles and metabolism. Dysfunction of CRY1 and CRY2 isoforms has been associated with a host of diseases, such as sleep phase disorder and metabolic diseases. Accumulating evidence for distinct roles of CRY1 and CRY2 has highlighted the need for CRY isoform-selective regulation; however, highly conserved sequences in CRY ligand-binding sites have hindered the design of isoform-selective compounds. Chemical biology approaches have been identifying small-molecule modulators of CRY proteins, which act in isoform-non-selective and also isoform-selective manners. In this review, we describe advances in our understanding of CRY isoform selectivity by comparing X-ray crystal structures of mammalian CRY isoforms in apo form and in complexes with compounds. We discuss how intrinsic conformational differences in identical residues of CRY1 and CRY2 contribute to unique interactions with different compound moieties for isoform selectivity.
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21
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Cryptochrome proteins regulate the circadian intracellular behavior and localization of PER2 in mouse suprachiasmatic nucleus neurons. Proc Natl Acad Sci U S A 2022; 119:2113845119. [PMID: 35046033 PMCID: PMC8795536 DOI: 10.1073/pnas.2113845119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
The suprachiasmatic nucleus (SCN), the master circadian clock of the mammalian brain, coordinates cellular clocks across the organism to regulate daily rhythms of physiology and behavior. SCN timekeeping pivots around transcriptional/translational feedback loops whereby PERIOD (PER) and CRYPTOCHROME (CRY) proteins associate and enter the nucleus to inhibit their own expression. The individual and interactive behaviors of PER and CRY and the mechanisms that regulate them are poorly understood. We combined fluorescence imaging of endogenous PER2 and viral vector–expressed CRY in SCN slices and show how CRYs, acting via their C terminus, control nuclear localization and mobility of PER2 to dose-dependently initiate SCN timekeeping and control its period. Our results reveal PER and CRY interactions central to the SCN clockwork. The ∼20,000 cells of the suprachiasmatic nucleus (SCN), the master circadian clock of the mammalian brain, coordinate subordinate cellular clocks across the organism, driving adaptive daily rhythms of physiology and behavior. The canonical model for SCN timekeeping pivots around transcriptional/translational feedback loops (TTFL) whereby PERIOD (PER) and CRYPTOCHROME (CRY) clock proteins associate and translocate to the nucleus to inhibit their own expression. The fundamental individual and interactive behaviors of PER and CRY in the SCN cellular environment and the mechanisms that regulate them are poorly understood. We therefore used confocal imaging to explore the behavior of endogenous PER2 in the SCN of PER2::Venus reporter mice, transduced with viral vectors expressing various forms of CRY1 and CRY2. In contrast to nuclear localization in wild-type SCN, in the absence of CRY proteins, PER2 was predominantly cytoplasmic and more mobile, as measured by fluorescence recovery after photobleaching. Virally expressed CRY1 or CRY2 relocalized PER2 to the nucleus, initiated SCN circadian rhythms, and determined their period. We used translational switching to control CRY1 cellular abundance and found that low levels of CRY1 resulted in minimal relocalization of PER2, but yet, remarkably, were sufficient to initiate and maintain circadian rhythmicity. Importantly, the C-terminal tail was necessary for CRY1 to localize PER2 to the nucleus and to initiate SCN rhythms. In CRY1-null SCN, CRY1Δtail opposed PER2 nuclear localization and correspondingly shortened SCN period. Through manipulation of CRY proteins, we have obtained insights into the spatiotemporal behaviors of PER and CRY sitting at the heart of the TTFL molecular mechanism.
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22
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Bolton CM, Bekaert M, Eilertsen M, Helvik JV, Migaud H. Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain. Front Physiol 2021; 12:761109. [PMID: 34925060 PMCID: PMC8674837 DOI: 10.3389/fphys.2021.761109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/09/2021] [Indexed: 12/28/2022] Open
Abstract
To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.
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Affiliation(s)
- Charlotte M Bolton
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Mariann Eilertsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jon Vidar Helvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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23
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Gul S, Rahim F, Isin S, Yilmaz F, Ozturk N, Turkay M, Kavakli IH. Structure-based design and classifications of small molecules regulating the circadian rhythm period. Sci Rep 2021; 11:18510. [PMID: 34531414 PMCID: PMC8445970 DOI: 10.1038/s41598-021-97962-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/27/2021] [Indexed: 11/09/2022] Open
Abstract
Circadian rhythm is an important mechanism that controls behavior and biochemical events based on 24 h rhythmicity. Ample evidence indicates disturbance of this mechanism is associated with different diseases such as cancer, mood disorders, and familial delayed phase sleep disorder. Therefore, drug discovery studies have been initiated using high throughput screening. Recently the crystal structures of core clock proteins (CLOCK/BMAL1, Cryptochromes (CRY), Periods), responsible for generating circadian rhythm, have been solved. Availability of structures makes amenable core clock proteins to design molecules regulating their activity by using in silico approaches. In addition to that, the implementation of classification features of molecules based on their toxicity and activity will improve the accuracy of the drug discovery process. Here, we identified 171 molecules that target functional domains of a core clock protein, CRY1, using structure-based drug design methods. We experimentally determined that 115 molecules were nontoxic, and 21 molecules significantly lengthened the period of circadian rhythm in U2OS cells. We then performed a machine learning study to classify these molecules for identifying features that make them toxic and lengthen the circadian period. Decision tree classifiers (DTC) identified 13 molecular descriptors, which predict the toxicity of molecules with a mean accuracy of 79.53% using tenfold cross-validation. Gradient boosting classifiers (XGBC) identified 10 molecular descriptors that predict and increase in the circadian period length with a mean accuracy of 86.56% with tenfold cross-validation. Our results suggested that these features can be used in QSAR studies to design novel nontoxic molecules that exhibit period lengthening activity.
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Affiliation(s)
- Seref Gul
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Fatih Rahim
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Safak Isin
- Department of Molecular Biology and Genetics, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Fatma Yilmaz
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
| | - Nuri Ozturk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
| | - Metin Turkay
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
| | - Ibrahim Halil Kavakli
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
- Department of Molecular Biology and Genetics, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
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24
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Chen H, Ding X, Ding E, Chen M, Wang H, Yang G, Zhu B. A missense variant rs2585405 in clock gene PER1 is associated with the increased risk of noise-induced hearing loss in a Chinese occupational population. BMC Med Genomics 2021; 14:221. [PMID: 34493277 PMCID: PMC8425122 DOI: 10.1186/s12920-021-01075-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE To investigate the potential association of cochlear clock genes (CRY1, CRY2, PER1, and PER2), the DNF gene (brain-derived neurotrophic factor), and the NTF3 gene (neurotrophin3) with susceptivity to noise-induced hearing loss (NIHL) among Chinese noise-exposed workers. METHODS A nested case-control study was performed with 2056 noise-exposed workers from a chemical fiber factory and an energy company who underwent occupational health examinations in 2019 as study subjects. Propensity score matching was conducted to screen cases and controls by matching sex, age, and the consumption of tobacco and alcohol. A total of 1269 participants were enrolled. Then, general information and noise exposure of the study subjects were obtained through a questionnaire survey and on-site noise detection. According to the results of audiological evaluations, the participants were divided into the case group (n = 432, high-frequency threshold shift > 25 dB) and the matched control group (n = 837, high-frequency threshold shift ≤ 25 dB) by propensity score matching. Genotyping for PER1 rs2253820 and rs2585405; PER2 rs56386336 and rs934945; CRY1 rs1056560 and rs3809236; CRY2 rs2292910 and rs6798; BDNF rs11030099, rs7124442 and rs6265; and NTF3 rs1805149 was conducted using the TaqMan-PCR technique. RESULTS In the dominant model and the co-dominant model, the distribution of PER1 rs2585405 genotypes between the case group and the control group was significantly different (P = 0.03, P = 0.01). The NIHL risk of the subjects with the GC genotype was 1.41 times the risk of those carrying the GG genotype (95% confidence interval (CI) of odds ratio (OR): 1.01-1.96), and the NIHL risk of the subjects with the CC genotype was 0.93 times the risk of those carrying the GG genotype (95%CI of OR: 0.71-1.21). After the noise exposure period and noise exposure intensities were stratified, in the co-dominant model, the adjusted OR values for noise intensities of ≤ 85 was 1.23 (95%CI: 0.99-1.53). In the dominant model, the adjusted OR values for noise exposure periods of ≤ 16 years and noise intensities of ≤ 85 were 1.88 (95%CI: 1.03-3.42) and 1.64 (95%CI: 1.12-2.38), respectively. CONCLUSION The CC/CG genotype of rs2585405 in the PER1 gene was identified as a potential risk factor for NIHL in Chinese noise-exposed workers, and interaction between rs2585405 and high temperature was found to be associated with NIHL risk.
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Affiliation(s)
- Hao Chen
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 210000, Jiangsu, China
| | - Xuexue Ding
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 210000, Jiangsu, China
| | - Enmin Ding
- Institute of Occupational Disease Prevention, Jiangsu Province Center for Disease Prevention and Control, Nanjing, 21009, Jiangsu, China
| | - Mengyao Chen
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 210000, Jiangsu, China
| | - Huimin Wang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210003, Jiangsu, China
| | - Guangzhi Yang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210003, Jiangsu, China
| | - Baoli Zhu
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 210000, Jiangsu, China.
- Institute of Occupational Disease Prevention, Jiangsu Province Center for Disease Prevention and Control, Nanjing, 21009, Jiangsu, China.
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25
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Abstract
Disruption of circadian rhythms increases the risk of several types of cancer. Mammalian cryptochromes (CRY1 and CRY2) are circadian transcriptional repressors that are related to DNA-repair enzymes. While CRYs lack DNA-repair activity, they modulate the transcriptional response to DNA damage, and CRY2 can promote SKP1 cullin 1-F-box (SCF)FBXL3-mediated ubiquitination of c-MYC and other targets. Here, we characterize five mutations in CRY2 observed in human cancers in The Cancer Genome Atlas. We demonstrate that two orthologous mutations of mouse CRY2 (D325H and S510L) accelerate the growth of primary mouse fibroblasts expressing high levels of c-MYC. Neither mutant affects steady-state levels of overexpressed c-MYC, and they have divergent impacts on circadian rhythms and on the ability of CRY2 to interact with SCFFBXL3 Unexpectedly, stable expression of either CRY2 D325H or of CRY2 S510L robustly suppresses P53 target-gene expression, suggesting that this may be a primary mechanism by which they influence cell growth.
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26
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Gabriel CH, Del Olmo M, Zehtabian A, Jäger M, Reischl S, van Dijk H, Ulbricht C, Rakhymzhan A, Korte T, Koller B, Grudziecki A, Maier B, Herrmann A, Niesner R, Zemojtel T, Ewers H, Granada AE, Herzel H, Kramer A. Live-cell imaging of circadian clock protein dynamics in CRISPR-generated knock-in cells. Nat Commun 2021; 12:3796. [PMID: 34145278 PMCID: PMC8213786 DOI: 10.1038/s41467-021-24086-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
The cell biology of circadian clocks is still in its infancy. Here, we describe an efficient strategy for generating knock-in reporter cell lines using CRISPR technology that is particularly useful for genes expressed transiently or at low levels, such as those coding for circadian clock proteins. We generated single and double knock-in cells with endogenously expressed PER2 and CRY1 fused to fluorescent proteins allowing us to simultaneously monitor the dynamics of CRY1 and PER2 proteins in live single cells. Both proteins are highly rhythmic in the nucleus of human cells with PER2 showing a much higher amplitude than CRY1. Surprisingly, CRY1 protein is nuclear at all circadian times indicating the absence of circadian gating of nuclear import. Furthermore, in the nucleus of individual cells CRY1 abundance rhythms are phase-delayed (~5 hours), and CRY1 levels are much higher (>5 times) compared to PER2 questioning the current model of the circadian oscillator.
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Affiliation(s)
- Christian H Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Marta Del Olmo
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Amin Zehtabian
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marten Jäger
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Silke Reischl
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Hannah van Dijk
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Carolin Ulbricht
- Immune Dynamics, Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Asylkhan Rakhymzhan
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Thomas Korte
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Barbara Koller
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Astrid Grudziecki
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Bert Maier
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Andreas Herrmann
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Raluca Niesner
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
- Dynamic and Functional in vivo Imaging, Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Adrián E Granada
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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27
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Karki N, Vergish S, Zoltowski BD. Cryptochromes: Photochemical and structural insight into magnetoreception. Protein Sci 2021; 30:1521-1534. [PMID: 33993574 DOI: 10.1002/pro.4124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
Abstract
Cryptochromes (CRYs) function as blue light photoreceptors in diverse physiological processes in nearly all kingdoms of life. Over the past several decades, they have emerged as the most likely candidates for light-dependent magnetoreception in animals, however, a long history of conflicts between in vitro photochemistry and in vivo behavioral data complicate validation of CRYs as a magnetosensor. In this review, we highlight the origins of conflicts regarding CRY photochemistry and signal transduction, and identify recent data that provides clarity on potential mechanisms of signal transduction in magnetoreception. The review primarily focuses on examining differences in photochemistry and signal transduction in plant and animal CRYs, and identifies potential modes of convergent evolution within these independent lineages that may identify conserved signaling pathways.
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Affiliation(s)
- Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Satyam Vergish
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
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28
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Crane BR. Winding Down: Selectively Drugging a Promiscuous Pocket in Cryptochrome Slows Circadian Rhythms. Cell Chem Biol 2021; 27:1109-1111. [PMID: 32946755 DOI: 10.1016/j.chembiol.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian cryptochromes regulate sleep and metabolism as components of the circadian clock. In this issue of Cell Chemical Biology, Miller et al. (2020a) use phenotypic chemical screens to identify selective modulators of two cryptochrome isoforms. Binding specificity depends on conformational patterning of the ligand-binding pocket and a disordered C-terminal domain.
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Affiliation(s)
- Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850 USA.
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29
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Nedrud D, Coyote-Maestas W, Schmidt D. A large-scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains. Proteins 2021; 89:899-914. [PMID: 33620761 DOI: 10.1002/prot.26067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022]
Abstract
Deep mutational scanning (DMS) facilitates data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering (SPINE) as a programmable DMS technique. We validate SPINE with a reference single mutant dataset in the PSD95 PDZ3 domain and then characterize most pairwise double mutants to study epistasis. We observe wide-spread proximal negative epistasis, which we attribute to mutations affecting thermodynamic stability, and strong long-range positive epistasis, which is enriched in an evolutionarily conserved and function-defining network of "sector" and clade-specifying residues. Conditional neutrality of mutations in clade-specifying residues compensates for deleterious mutations in sector positions. This suggests that epistatic interactions between these position pairs facilitated the evolutionary expansion and specialization of PDZ domains. We propose that SPINE provides easy experimental access to reveal epistasis signatures in proteins that will improve our understanding of the structural basis for protein function and adaptation.
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Affiliation(s)
- David Nedrud
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Willow Coyote-Maestas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, Minnesota, USA
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30
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Bantle CM, French CT, Cummings JE, Sadasivan S, Tran K, Slayden RA, Smeyne RJ, Tjalkens RB. Manganese exposure in juvenile C57BL/6 mice increases glial inflammatory responses in the substantia nigra following infection with H1N1 influenza virus. PLoS One 2021; 16:e0245171. [PMID: 33493177 PMCID: PMC7833173 DOI: 10.1371/journal.pone.0245171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/22/2020] [Indexed: 01/22/2023] Open
Abstract
Infection with Influenza A virus can lead to the development of encephalitis and subsequent neurological deficits ranging from headaches to neurodegeneration. Post-encephalitic parkinsonism has been reported in surviving patients of H1N1 infections, but not all cases of encephalitic H1N1 infection present with these neurological symptoms, suggesting that interactions with an environmental neurotoxin could promote more severe neurological damage. The heavy metal, manganese (Mn), is a potential interacting factor with H1N1 because excessive exposure early in life can induce long-lasting effects on neurological function through inflammatory activation of glial cells. In the current study, we used a two-hit model of neurotoxin-pathogen exposure to examine whether exposure to Mn during juvenile development would induce a more severe neuropathological response following infection with H1N1 in adulthood. To test this hypothesis, C57BL/6 mice were exposed to MnCl2 in drinking water (50 mg/kg/day) for 30 days from days 21–51 postnatal, then infected intranasally with H1N1 three weeks later. Analyses of dopaminergic neurons, microglia and astrocytes in basal ganglia indicated that although there was no significant loss of dopaminergic neurons within the substantia nigra pars compacta, there was more pronounced activation of microglia and astrocytes in animals sequentially exposed to Mn and H1N1, as well as altered patterns of histone acetylation. Whole transcriptome Next Generation Sequencing (RNASeq) analysis was performed on the substantia nigra and revealed unique patterns of gene expression in the dual-exposed group, including genes involved in antioxidant activation, mitophagy and neurodegeneration. Taken together, these results suggest that exposure to elevated levels of Mn during juvenile development could sensitize glial cells to more severe neuro-immune responses to influenza infection later in life through persistent epigenetic changes.
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Affiliation(s)
- Collin M. Bantle
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - C. Tenley French
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jason E. Cummings
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Shankar Sadasivan
- Department of Neuroscience, Vickie & Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Kevin Tran
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Richard A. Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Richard J. Smeyne
- Department of Neuroscience, Vickie & Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Ronald B. Tjalkens
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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31
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Kolarski D, Miller S, Oshima T, Nagai Y, Aoki Y, Kobauri P, Srivastava A, Sugiyama A, Amaike K, Sato A, Tama F, Szymanski W, Feringa BL, Itami K, Hirota T. Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock. J Am Chem Soc 2021; 143:2078-2087. [PMID: 33464888 PMCID: PMC7863067 DOI: 10.1021/jacs.0c12280] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
CRY1
and CRY2 proteins are highly conserved components of the circadian
clock that controls daily physiological rhythms. Disruption of CRY
functions are related to many diseases, including circadian sleep
phase disorder. Development of isoform-selective and spatiotemporally
controllable tools will facilitate the understanding of shared and
distinct functions of CRY1 and CRY2. Here, we developed CRY1-selective
compounds that enable light-dependent manipulation of the circadian
clock. From phenotypic chemical screening in human cells, we identified
benzophenone derivatives that lengthened the circadian period. These
compounds selectively interacted with the CRY1 photolyase homology
region, resulting in activation of CRY1 but not CRY2. The benzophenone
moiety rearranged a CRY1 region called the “lid loop”
located outside of the compound-binding pocket and formed a unique
interaction with Phe409 in the lid loop. Manipulation of this key
interaction was achieved by rationally designed replacement of the
benzophenone with a switchable azobenzene moiety whose cis–trans isomerization can be controlled by light. The metastable cis form exhibited sufficiently high half-life in aqueous
solutions and structurally mimicked the benzophenone unit, enabling
reversible period regulation over days by cellular irradiation with
visible light. This study revealed an unprecedented role of the lid
loop in CRY-compound interaction and paves the way for spatiotemporal
regulation of CRY1 activity by photopharmacology for molecular understanding
of CRY1-dependent functions in health and disease.
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Affiliation(s)
- Dušan Kolarski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Yugo Aoki
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Piermichele Kobauri
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Ashutosh Srivastava
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Kazuma Amaike
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan.,Computational Structural Biology Unit, RIKEN-Center for Computational Science, Hyogo 650-0047, Japan
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands.,Department of Radiology, Medical Imaging Center, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
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32
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Molecular mechanism of the repressive phase of the mammalian circadian clock. Proc Natl Acad Sci U S A 2020; 118:2021174118. [PMID: 33443219 DOI: 10.1073/pnas.2021174118] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The mammalian circadian clock consists of a transcription-translation feedback loop (TTFL) composed of CLOCK-BMAL1 transcriptional activators and CRY-PER transcriptional repressors. Previous work showed that CRY inhibits CLOCK-BMAL1-activated transcription by a "blocking"-type mechanism and that CRY-PER inhibits CLOCK-BMAL1 by a "displacement"-type mechanism. While the mechanism of CRY-mediated repression was explained by both in vitro and in vivo experiments, the CRY-PER-mediated repression in vivo seemed in conflict with the in vitro data demonstrating PER removes CRY from the CLOCK-BMAL1-E-box complex. Here, we show that CRY-PER participates in the displacement-type repression by recruiting CK1δ to the nucleus and mediating an increased local concentration of CK1δ at CLOCK-BMAL1-bound promoters/enhancers and thus promoting the phosphorylation of CLOCK and dissociation of CLOCK-BMAL1 along with CRY from the E-box. Our findings bring clarity to the role of PER in the dynamic nature of the repressive phase of the TTFL.
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33
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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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34
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A structurally conserved human and Tetrahymena telomerase catalytic core. Proc Natl Acad Sci U S A 2020; 117:31078-31087. [PMID: 33229538 DOI: 10.1073/pnas.2011684117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Telomerase is a ribonucleoprotein complex that counteracts the shortening of chromosome ends due to incomplete replication. Telomerase contains a catalytic core of telomerase reverse transcriptase (TERT) and telomerase RNA (TER). However, what defines TERT and separates it from other reverse transcriptases remains a subject of debate. A recent cryoelectron microscopy map of Tetrahymena telomerase revealed the structure of a previously uncharacterized TERT domain (TRAP) with unanticipated interactions with the telomerase essential N-terminal (TEN) domain and roles in telomerase activity. Both TEN and TRAP are absent in the putative Tribolium TERT that has been used as a model for telomerase for over a decade. To investigate the conservation of TRAP and TEN across species, we performed multiple sequence alignments and statistical coupling analysis on all identified TERTs and find that TEN and TRAP have coevolved as telomerase-specific domains. Integrating the data from bioinformatic analysis and the structure of Tetrahymena telomerase, we built a pseudoatomic model of human telomerase catalytic core that accounts for almost all of the cryoelectron microscopy density in a published map, including TRAP in previously unassigned density as well as telomerase RNA domains essential for activity. This more complete model of the human telomerase catalytic core illustrates how domains of TER and TERT, including the TEN-TRAP complex, can interact in a conserved manner to regulate telomere synthesis.
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35
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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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36
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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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37
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Liu H, Su T, He W, Wang Q, Lin C. The Universally Conserved Residues Are Not Universally Required for Stable Protein Expression or Functions of Cryptochromes. Mol Biol Evol 2020; 37:327-340. [PMID: 31550045 DOI: 10.1093/molbev/msz217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Universally conserved residues (UCRs) are invariable amino acids evolutionarily conserved among members of a protein family across diverse kingdoms of life. UCRs are considered important for stability and/or function of protein families, but it has not been experimentally examined systematically. Cryptochromes are photoreceptors in plants or light-independent components of the circadian clocks in mammals. We experimentally analyzed 51 UCRs of Arabidopsis cryptochrome 2 (CRY2) that are universally conserved in eukaryotic cryptochromes from Arabidopsis to human. Surprisingly, we found that UCRs required for stable protein expression of CRY2 in plants are not similarly required for stable protein expression of human hCRY1 in human cells. Moreover, 74% of the stably expressed CRY2 proteins mutated in UCRs retained wild-type-like activities for at least one photoresponses analyzed. Our finding suggests that the evolutionary mechanisms underlying conservation of UCRs or that distinguish UCRs from non-UCRs determining the same functions of individual cryptochromes remain to be investigated.
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Affiliation(s)
- Huachun Liu
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA
| | - Tiantian Su
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA.,UCLA-FAFU Joint Research Center on Plant Proteomics, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjin He
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA.,College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qin Wang
- UCLA-FAFU Joint Research Center on Plant Proteomics, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA
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38
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Crosby P, Partch CL. New insights into non-transcriptional regulation of mammalian core clock proteins. J Cell Sci 2020; 133:133/18/jcs241174. [PMID: 32934011 DOI: 10.1242/jcs.241174] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mammalian circadian rhythms drive ∼24 h periodicity in a wide range of cellular processes, temporally coordinating physiology and behaviour within an organism, and synchronising this with the external day-night cycle. The canonical model for this timekeeping consists of a delayed negative-feedback loop, containing transcriptional activator complex CLOCK-BMAL1 (BMAL1 is also known as ARNTL) and repressors period 1, 2 and 3 (PER1, PER2 and PER3) and cryptochrome 1 and 2 (CRY1 and CRY2), along with a number of accessory factors. Although the broad strokes of this system are defined, the exact molecular mechanisms by which these proteins generate a self-sustained rhythm with such periodicity and fidelity remains a topic of much research. Recent studies have identified prominent roles for a number of crucial post-transcriptional, translational and, particularly, post-translational events within the mammalian circadian oscillator, providing an increasingly complex understanding of the activities and interactions of the core clock proteins. In this Review, we highlight such contemporary work on non-transcriptional events and set it within our current understanding of cellular circadian timekeeping.
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Affiliation(s)
- Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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Abstract
Circadian clocks are cell-autonomous self-sustaining oscillators that allow organisms to anticipate environmental changes throughout the solar day and persist in nearly every cell examined. Environmental or genetic disruption of circadian rhythms increases the risk of several types of cancer, but the underlying mechanisms are not well understood. Here, we discuss evidence connecting circadian rhythms-with emphasis on the cryptochrome proteins (CRY1/2)-to cancer through in vivo models, mechanisms involving known tumor suppressors and oncogenes, chemotherapeutic efficacy, and human cancer risk.
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Affiliation(s)
- Alanna B Chan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Katja A Lamia
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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40
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Vaughan ME, Wallace M, Handzlik MK, Chan AB, Metallo CM, Lamia KA. Cryptochromes Suppress HIF1α in Muscles. iScience 2020; 23:101338. [PMID: 32683313 PMCID: PMC7371909 DOI: 10.1016/j.isci.2020.101338] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/13/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
Muscles preferentially utilize glycolytic or oxidative metabolism depending on the intensity of physical activity. Transcripts required for carbohydrate and lipid metabolism undergo circadian oscillations of expression in muscles, and both exercise capacity and the metabolic response to exercise are influenced by time of day. The circadian repressors CRY1 and CRY2 repress peroxisome proliferator-activated receptor delta (PPARδ), a major driver of oxidative metabolism and exercise endurance. CRY-deficient mice exhibit enhanced PPARδ activation and greater maximum speed when running on a treadmill but no increase in exercise endurance. Here we demonstrate that CRYs limit hypoxia-responsive transcription via repression of HIF1α-BMAL1 heterodimers. Furthermore, CRY2 appeared to be more effective than CRY1 in the reduction of HIF1α protein steady-state levels in primary myotubes and quadriceps in vivo. Finally, CRY-deficient myotubes exhibit metabolic alterations consistent with cryptochrome-dependent suppression of HIF1α, which likely contributes to circadian modulation of muscle metabolism. CRY2 plays a unique role in regulating HIF1α protein accumulation in muscle HIF1α and BMAL1 heterodimers are transcriptionally active CRY1/2 represses transcription driven by HIF1α/BMAL1 heterodimers Cryptochromes influence skeletal muscle substrate preference and utilization
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Affiliation(s)
- Megan E Vaughan
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Martina Wallace
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michal K Handzlik
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alanna B Chan
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katja A Lamia
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.
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41
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42
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Ju D, Zhang W, Yan J, Zhao H, Li W, Wang J, Liao M, Xu Z, Wang Z, Zhou G, Mei L, Hou N, Ying S, Cai T, Chen S, Xie X, Lai L, Tang C, Park N, Takahashi JS, Huang N, Qi X, Zhang EE. Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Sci Transl Med 2020; 12:12/542/eaba0769. [DOI: 10.1126/scitranslmed.aba0769] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 04/13/2020] [Indexed: 12/12/2022]
Abstract
Transcriptional regulation lies at the core of the circadian clockwork, but how the clock-related transcription machinery controls the circadian phase is not understood. Here, we show both in human cells and in mice that RuvB-like ATPase 2 (RUVBL2) interacts with other known clock proteins on chromatin to regulate the circadian phase. Pharmacological perturbation of RUVBL2 with the adenosine analog compound cordycepin resulted in a rapid-onset 12-hour clock phase-shift phenotype at human cell, mouse tissue, and whole-animal live imaging levels. Using simple peripheral injection treatment, we found that cordycepin penetrated the blood-brain barrier and caused rapid entrainment of the circadian phase, facilitating reduced duration of recovery in a mouse jet-lag model. We solved a crystal structure for human RUVBL2 in complex with a physiological metabolite of cordycepin, and biochemical assays showed that cordycepin treatment caused disassembly of an interaction between RUVBL2 and the core clock component BMAL1. Moreover, we showed with spike-in ChIP-seq analysis and binding assays that cordycepin treatment caused disassembly of the circadian super-complex, which normally resides at E-box chromatin loci such as PER1, PER2, DBP, and NR1D1. Mathematical modeling supported that the observed type 0 phase shifts resulted from derepression of E-box clock gene transcription.
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Affiliation(s)
- Dapeng Ju
- National Institute of Biological Sciences, Beijing 102206, China
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Zhang
- RPXDs (Suzhou) Co. Ltd., Suzhou City, Jiangsu Province 215028, China
| | - Jiawei Yan
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Haijiao Zhao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wei Li
- RPXDs (Suzhou) Co. Ltd., Suzhou City, Jiangsu Province 215028, China
| | - Jiawen Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meimei Liao
- National Institute of Biological Sciences, Beijing 102206, China
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhancong Xu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhiqiang Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Guanshen Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - Long Mei
- National Institute of Biological Sciences, Beijing 102206, China
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Nannan Hou
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shuhua Ying
- National Institute of Biological Sciences, Beijing 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaowen Xie
- School of Life Sciences, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- School of Physics and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Noheon Park
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Joseph S. Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Niu Huang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Eric Erquan Zhang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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43
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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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44
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Miller S, Son YL, Aikawa Y, Makino E, Nagai Y, Srivastava A, Oshima T, Sugiyama A, Hara A, Abe K, Hirata K, Oishi S, Hagihara S, Sato A, Tama F, Itami K, Kay SA, Hatori M, Hirota T. Isoform-selective regulation of mammalian cryptochromes. Nat Chem Biol 2020; 16:676-685. [PMID: 32231341 DOI: 10.1038/s41589-020-0505-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
CRY1 and CRY2 are essential components of the circadian clock controlling daily physiological rhythms. Accumulating evidences indicate distinct roles of these highly homologous proteins, in addition to redundant functions. Therefore, the development of isoform-selective compounds represents an effective approach towards understanding the similarities and differences of CRY1 and CRY2 by controlling each isoform individually. We conducted phenotypic screenings of circadian clock modulators, and identified KL101 and TH301 that selectively stabilize CRY1 and CRY2, respectively. Crystal structures of CRY-compound complexes revealed conservation of compound-binding sites between CRY1 and CRY2. We further discovered a unique mechanism underlying compound selectivity in which the disordered C-terminal region outside the pocket was required for the differential effects of KL101 and TH301 against CRY isoforms. By using these compounds, we found a new role of CRY1 and CRY2 as enhancers of brown adipocyte differentiation, providing the basis of CRY-mediated regulation of energy expenditure.
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Affiliation(s)
- Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - You Lee Son
- Laboratory of Chronobiology, Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yoshiki Aikawa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Eri Makino
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | | | - Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Aya Hara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan
| | | | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,Computational Structural Biology Unit, RIKEN-Center for Computational Science, Hyogo, Japan
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Megumi Hatori
- Laboratory of Chronobiology, Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan.
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.
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45
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Jiao W, Fan Y, Blackmore NJ, Parker EJ. A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis. J Biol Chem 2020; 295:6252-6262. [PMID: 32217694 DOI: 10.1074/jbc.ra120.012605] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/20/2020] [Indexed: 01/08/2023] Open
Abstract
Allostery exploits the conformational dynamics of enzymes by triggering a shift in population ensembles toward functionally distinct conformational or dynamic states. Allostery extensively regulates the activities of key enzymes within biosynthetic pathways to meet metabolic demand for their end products. Here, we have examined a critical enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS), at the gateway to aromatic amino acid biosynthesis in Mycobacterium tuberculosis, which shows extremely complex dynamic allostery: three distinct aromatic amino acids jointly communicate occupancy to the active site via subtle changes in dynamics, enabling exquisite fine-tuning of delivery of these essential metabolites. Furthermore, this allosteric mechanism is co-opted by pathway branchpoint enzyme chorismate mutase upon complex formation. In this study, using statistical coupling analysis, site-directed mutagenesis, isothermal calorimetry, small-angle X-ray scattering, and X-ray crystallography analyses, we have pinpointed a critical node within the complex dynamic communication network responsible for this sophisticated allosteric machinery. Through a facile Gly to Pro substitution, we have altered backbone dynamics, completely severing the allosteric signal yet remarkably, generating a nonallosteric enzyme that retains full catalytic activity. We also identified a second residue of prime importance to the inter-enzyme communication with chorismate mutase. Our results reveal that highly complex dynamic allostery is surprisingly vulnerable and provide further insights into the intimate link between catalysis and allostery.
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Affiliation(s)
- Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Yifei Fan
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Nicola J Blackmore
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand .,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
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46
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Vanderstraeten J, Gailly P, Malkemper EP. Light entrainment of retinal biorhythms: cryptochrome 2 as candidate photoreceptor in mammals. Cell Mol Life Sci 2020; 77:875-884. [PMID: 31982933 PMCID: PMC11104904 DOI: 10.1007/s00018-020-03463-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 12/31/2022]
Abstract
The mechanisms that synchronize the biorhythms of the mammalian retina with the light/dark cycle are independent of those synchronizing the rhythms in the central pacemaker, the suprachiasmatic nucleus. The identity of the photoreceptor(s) responsible for the light entrainment of the retina of mammals is still a matter of debate, and recent studies have reported contradictory results in this respect. Here, we suggest that cryptochromes (CRY), in particular CRY 2, are involved in that light entrainment. CRY are highly conserved proteins that are a key component of the cellular circadian clock machinery. In plants and insects, they are responsible for the light entrainment of these biorhythms, mediated by the light response of their flavin cofactor (FAD). In mammals, however, no light-dependent role is currently assumed for CRY in light-exposed tissues, including the retina. It has been reported that FAD influences the function of mammalian CRY 2 and that human CRY 2 responds to light in Drosophila, suggesting that mammalian CRY 2 keeps the ability to respond to light. Here, we hypothesize that CRY 2 plays a role in the light entrainment of retinal biorhythms, at least in diurnal mammals. Indeed, published data shows that the light intensity dependence and the wavelength sensitivity commonly reported for that light entrainment fits the light sensitivity and absorption spectrum of light-responsive CRY. We propose experiments to test our hypothesis and to further explore the still-pending question of the function of CRY 2 in the mammalian retina.
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Affiliation(s)
- Jacques Vanderstraeten
- Faculty of Medicine, School of Public Health, Environmental and Work Health Research Center, Université Libre de Bruxelles, CP593, Route de Lennik, 808, 1070, Brussels, Belgium.
- , Avenue Constant Montald, 11, 1200, Brussels, Belgium.
| | - Philippe Gailly
- Faculty of Medicine, Institute of Neuroscience (IONS), Cellular and Molecular Pole (CEMO), Catholic University of Louvain, Avenue Mounier 53/B1.53.17, 1200, Brussels, Belgium
| | - E Pascal Malkemper
- Center of Advanced European Studies and Research (CAESAR), Ludwig-Erhard-Allee 2, Bonn, 53175, Germany
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47
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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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48
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. TRENDS IN PLANT SCIENCE 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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49
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Cox KH, Takahashi JS. Circadian clock genes and the transcriptional architecture of the clock mechanism. J Mol Endocrinol 2019; 63:R93-R102. [PMID: 31557726 PMCID: PMC6872945 DOI: 10.1530/jme-19-0153] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022]
Abstract
The mammalian circadian clock has evolved as an adaptation to the 24-h light/darkness cycle on earth. Maintaining cellular activities in synchrony with the activities of the organism (such as eating and sleeping) helps different tissue and organ systems coordinate and optimize their performance. The full extent of the mechanisms by which cells maintain the clock are still under investigation, but involve a core set of clock genes that regulate large networks of gene transcription both by direct transcriptional activation/repression as well as the recruitment of proteins that modify chromatin states more broadly.
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Affiliation(s)
- Kimberly H. Cox
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Joseph S. Takahashi
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
- To whom correspondence should be addressed:
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50
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Zoltowski BD, Chelliah Y, Wickramaratne A, Jarocha L, Karki N, Xu W, Mouritsen H, Hore PJ, Hibbs RE, Green CB, Takahashi JS. Chemical and structural analysis of a photoactive vertebrate cryptochrome from pigeon. Proc Natl Acad Sci U S A 2019; 116:19449-19457. [PMID: 31484780 PMCID: PMC6765304 DOI: 10.1073/pnas.1907875116] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Computational and biochemical studies implicate the blue-light sensor cryptochrome (CRY) as an endogenous light-dependent magnetosensor enabling migratory birds to navigate using the Earth's magnetic field. Validation of such a mechanism has been hampered by the absence of structures of vertebrate CRYs that have functional photochemistry. Here we present crystal structures of Columba livia (pigeon) CRY4 that reveal evolutionarily conserved modifications to a sequence of Trp residues (Trp-triad) required for CRY photoreduction. In ClCRY4, the Trp-triad chain is extended to include a fourth Trp (W369) and a Tyr (Y319) residue at the protein surface that imparts an unusually high quantum yield of photoreduction. These results are consistent with observations of night migratory behavior in animals at low light levels and could have implications for photochemical pathways allowing magnetosensing.
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Affiliation(s)
- Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275
- Center for Drug Discovery, Design, and Delivery, Southern Methodist University, Dallas, TX 75275
| | - Yogarany Chelliah
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Anushka Wickramaratne
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lauren Jarocha
- Department of Chemistry, University of Oxford, OX1 3QZ Oxford, United Kingdom
| | - Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275
- Center for Drug Discovery, Design, and Delivery, Southern Methodist University, Dallas, TX 75275
| | - Wei Xu
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Henrik Mouritsen
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, DE-26111 Oldenburg, Germany
- Research Center for Neurosensory Sciences, University of Oldenburg, DE-26111 Oldenburg, Germany
| | - Peter J Hore
- Department of Chemistry, University of Oxford, OX1 3QZ Oxford, United Kingdom
| | - Ryan E Hibbs
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390;
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
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