1
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Nolan RB, Fan JY, Price JL. Circadian rhythms in the Drosophila eye may regulate adaptation of vision to light intensity. Front Neurosci 2024; 18:1401721. [PMID: 38872947 PMCID: PMC11169718 DOI: 10.3389/fnins.2024.1401721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
The sensitivity of the eye at night would lead to complete saturation of the eye during the day. Therefore, the sensitivity of the eye must be down-regulated during the day to maintain visual acuity. In the Drosophila eye, the opening of TRP and TRPL channels leads to an influx of Ca++ that triggers down-regulation of further responses to light, including the movement of the TRPL channel and Gα proteins out of signaling complexes found in actin-mediated microvillar extensions of the photoreceptor cells (the rhabdomere). The eye also exhibits a light entrained-circadian rhythm, and we have recently observed that one component of this rhythm (BDBT) becomes undetectable by antibodies after exposure to light even though immunoblot analyses still detect it in the eye. BDBT is necessary for normal circadian rhythms, and in several circadian and visual mutants this eye-specific oscillation of detection is lost. Many phototransduction signaling proteins (e.g., Rhodopsin, TRP channels and Gα) also become undetectable shortly after light exposure, most likely due to a light-induced compaction of the rhabdomeric microvilli. The circadian protein BDBT might be involved in light-induced changes in the rhabdomere, and if so this could indicate that circadian clocks contribute to the daily adaptations of the eye to light. Likewise, circadian oscillations of clock proteins are observed in photoreceptors of the mammalian eye and produce a circadian oscillation in the ERG. Disruption of circadian rhythms in the eyes of mammals causes neurodegeneration in the eye, demonstrating the importance of the rhythms for normal eye function.
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Affiliation(s)
| | | | - Jeffrey L. Price
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri – Kansas City, Kansas City, MO, United States
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2
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Del Olmo M, Legewie S, Brunner M, Höfer T, Kramer A, Blüthgen N, Herzel H. Network switches and their role in circadian clocks. J Biol Chem 2024; 300:107220. [PMID: 38522517 PMCID: PMC11044057 DOI: 10.1016/j.jbc.2024.107220] [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: 07/03/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Circadian rhythms are generated by complex interactions among genes and proteins. Self-sustained ∼24 h oscillations require negative feedback loops and sufficiently strong nonlinearities that are the product of molecular and network switches. Here, we review common mechanisms to obtain switch-like behavior, including cooperativity, antagonistic enzymes, multisite phosphorylation, positive feedback, and sequestration. We discuss how network switches play a crucial role as essential components in cellular circadian clocks, serving as integral parts of transcription-translation feedback loops that form the basis of circadian rhythm generation. The design principles of network switches and circadian clocks are illustrated by representative mathematical models that include bistable systems and negative feedback loops combined with Hill functions. This work underscores the importance of negative feedback loops and network switches as essential design principles for biological oscillations, emphasizing how an understanding of theoretical concepts can provide insights into the mechanisms generating biological rhythms.
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Affiliation(s)
- Marta Del Olmo
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Michael Brunner
- Biochemistry Center, Universität Heidelberg, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Universität Heidelberg, Heidelberg, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
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3
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Heaney J, Zhao J, Casagranda F, Loveland KL, Siddall NA, Hime GR. Drosophila Importin Alpha 1 (Dα1) Is Required to Maintain Germline Stem Cells in the Testis Niche. Cells 2024; 13:494. [PMID: 38534338 DOI: 10.3390/cells13060494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Stem cell maintenance and differentiation can be regulated via the differential activity of transcription factors within stem cells and their progeny. For these factors to be active, they need to be transported from their site of synthesis in the cytoplasm into the nucleus. A tissue-specific requirement for factors involved in nuclear importation is a potential mechanism to regulate stem cell differentiation. We have undertaken a characterization of male sterile importin alpha 1 (Dα1) null alleles in Drosophila and found that Dα1 is required for maintaining germline stem cells (GSCs) in the testis niche. The loss of GSCs can be rescued by ectopic expression of Dα1 within the germline but the animals are still infertile, indicating a second role for Dα1 in spermatogenesis. Expression of a Dα1 dominant negative transgene in GSCs confirmed a functional requirement for Dα1 in GSC maintenance but expression of the transgene in differentiating spermatogonia did not exhibit a phenotype indicating a specific role for Dα1 within GSCs. Our data indicate that Dα1 is utilized as a regulatory protein within GSCs to facilitate nuclear importation of proteins that maintain the stem cell pool.
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Affiliation(s)
- James Heaney
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jiamin Zhao
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Franca Casagranda
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kate L Loveland
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
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4
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Mao J, Cao Y, Zhang Y, Huang B, Zhao Y. A novel method for identifying key genes in macroevolution based on deep learning with attention mechanism. Sci Rep 2023; 13:19727. [PMID: 37957311 PMCID: PMC10643560 DOI: 10.1038/s41598-023-47113-9] [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: 06/27/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023] Open
Abstract
Macroevolution can be regarded as the result of evolutionary changes of synergistically acting genes. Unfortunately, the importance of these genes in macroevolution is difficult to assess and hence the identification of macroevolutionary key genes is a major challenge in evolutionary biology. In this study, we designed various word embedding libraries of natural language processing (NLP) considering the multiple mechanisms of evolutionary genomics. A novel method (IKGM) based on three types of attention mechanisms (domain attention, kmer attention and fused attention) were proposed to calculate the weights of different genes in macroevolution. Taking 34 species of diurnal butterflies and nocturnal moths in Lepidoptera as an example, we identified a few of key genes with high weights, which annotated to the functions of circadian rhythms, sensory organs, as well as behavioral habits etc. This study not only provides a novel method to identify the key genes of macroevolution at the genomic level, but also helps us to understand the microevolution mechanisms of diurnal butterflies and nocturnal moths in Lepidoptera.
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Affiliation(s)
- Jiawei Mao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China
| | - Yong Cao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China
| | - Yan Zhang
- College of Mathematics and Physics, Southwest Forestry University, Kunming, 650224, China
| | - Biaosheng Huang
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China
| | - Youjie Zhao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China.
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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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Tabuloc CA, Cai YD, Kwok RS, Chan EC, Hidalgo S, Chiu JC. CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters. PLoS Genet 2023; 19:e1010649. [PMID: 36809369 PMCID: PMC9983840 DOI: 10.1371/journal.pgen.1010649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/03/2023] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Circadian clock and chromatin-remodeling complexes are tightly intertwined systems that regulate rhythmic gene expression. The circadian clock promotes rhythmic expression, timely recruitment, and/or activation of chromatin remodelers, while chromatin remodelers regulate accessibility of clock transcription factors to the DNA to influence expression of clock genes. We previously reported that the BRAHMA (BRM) chromatin-remodeling complex promotes the repression of circadian gene expression in Drosophila. In this study, we investigated the mechanisms by which the circadian clock feeds back to modulate daily BRM activity. Using chromatin immunoprecipitation, we observed rhythmic BRM binding to clock gene promoters despite constitutive BRM protein expression, suggesting that factors other than protein abundance are responsible for rhythmic BRM occupancy at clock-controlled loci. Since we previously reported that BRM interacts with two key clock proteins, CLOCK (CLK) and TIMELESS (TIM), we examined their effect on BRM occupancy to the period (per) promoter. We observed reduced BRM binding to the DNA in clk null flies, suggesting that CLK is involved in enhancing BRM occupancy to initiate transcriptional repression at the conclusion of the activation phase. Additionally, we observed reduced BRM binding to the per promoter in flies overexpressing TIM, suggesting that TIM promotes BRM removal from DNA. These conclusions are further supported by elevated BRM binding to the per promoter in flies subjected to constant light and experiments in Drosophila tissue culture in which the levels of CLK and TIM are manipulated. In summary, this study provides new insights into the reciprocal regulation between the circadian clock and the BRM chromatin-remodeling complex.
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Affiliation(s)
- Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Rosanna S. Kwok
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Elizabeth C. Chan
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
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7
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Thakkar N, Giesecke A, Bazalova O, Martinek J, Smykal V, Stanewsky R, Dolezel D. Evolution of casein kinase 1 and functional analysis of new doubletime mutants in Drosophila. Front Physiol 2022; 13:1062632. [PMID: 36589447 PMCID: PMC9794997 DOI: 10.3389/fphys.2022.1062632] [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: 10/06/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Circadian clocks are timing devices that rhythmically adjust organism's behavior, physiology, and metabolism to the 24-h day-night cycle. Eukaryotic circadian clocks rely on several interlocked transcription-translation feedback loops, where protein stability is the key part of the delay between transcription and the appearance of the mature proteins within the feedback loops. In bilaterian animals, including mammals and insects, the circadian clock depends on a homologous set of proteins. Despite mostly conserved clock components among the fruit fly Drosophila and mammals, several lineage-specific differences exist. Here we have systematically explored the evolution and sequence variability of insect DBT proteins and their vertebrate homologs casein kinase 1 delta (CKIδ) and epsilon (CKIε), dated the origin and separation of CKIδ from CKIε, and identified at least three additional independent duplications of the CKIδ/ε gene in Petromyzon, Danio, and Xenopus. We determined conserved regions in DBT specific to Diptera, and functionally tested a subset of those in D. melanogaster. Replacement of Lysine K224 with acidic residues strongly impacts the free-running period even in heterozygous flies, whereas homozygous mutants are not viable. K224D mutants have a temperature compensation defect with longer free-running periods at higher temperatures, which is exactly the opposite trend of what was reported for corresponding mammalian mutants. All DBTs of dipteran insects contain the NKRQK motif at positions 220-224. The occurrence of this motif perfectly correlates with the presence of BRIDE OF DOUBLETIME, BDBT, in Diptera. BDBT is a non-canonical FK506-binding protein that physically interacts with Drosophila DBT. The phylogeny of FK506-binding proteins suggests that BDBT is either absent or highly modified in non-dipteran insects. In addition to in silico analysis of DBT/CKIδ/ε evolution and diversity, we have identified four novel casein kinase 1 genes specific to the Drosophila genus.
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Affiliation(s)
- Nirav Thakkar
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Astrid Giesecke
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Olga Bazalova
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Jan Martinek
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Vlastimil Smykal
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany,*Correspondence: Ralf Stanewsky, ; David Dolezel,
| | - David Dolezel
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia,*Correspondence: Ralf Stanewsky, ; David Dolezel,
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8
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Ribeiro IMA, Eßbauer W, Kutlesa R, Borst A. Spatial and temporal control of expression with light-gated LOV-LexA. G3 GENES|GENOMES|GENETICS 2022; 12:6649684. [PMID: 35876796 PMCID: PMC9526042 DOI: 10.1093/g3journal/jkac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022]
Abstract
The ability to drive expression of exogenous genes in different tissues and cell types, under the control of specific enhancers, has been crucial for discovery in biology. While many enhancers drive expression broadly, several genetic tools were developed to obtain access to isolated cell types. Studies of spatially organized neuropiles in the central nervous system of fruit flies have raised the need for a system that targets subsets of cells within a single neuronal type, a feat currently dependent on stochastic flip-out methods. To access the same cells within a given expression pattern consistently across fruit flies, we developed the light-gated expression system LOV-LexA. We combined the bacterial LexA transcription factor with the plant-derived light, oxygen, or voltage photosensitive domain and a fluorescent protein. Exposure to blue light uncages a nuclear localizing signal in the C-terminal of the light, oxygen, or voltage domain and leads to the translocation of LOV-LexA to the nucleus, with the subsequent initiation of transcription. LOV-LexA enables spatial and temporal control of expression of transgenes under LexAop sequences in larval fat body and pupal and adult neurons with blue light. The LOV-LexA tool is ready to use with GAL4 and Split-GAL4 drivers in its current form and constitutes another layer of intersectional genetics that provides light-controlled genetic access to specific cells across flies.
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Affiliation(s)
- Inês M A Ribeiro
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Wolfgang Eßbauer
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Romina Kutlesa
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
| | - Alexander Borst
- Department of Circuits-Computations-Models, Max Planck Institute of Neurobiology , 82152 Martinsried, Germany
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9
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Fang Y, Gu Y. Regulation of Plant Immunity by Nuclear Membrane-Associated Mechanisms. Front Immunol 2021; 12:771065. [PMID: 34938291 PMCID: PMC8685260 DOI: 10.3389/fimmu.2021.771065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/18/2021] [Indexed: 12/25/2022] Open
Abstract
Unlike animals, plants do not have specialized immune cells and lack an adaptive immune system. Instead, plant cells rely on their unique innate immune system to defend against pathogens and coordinate beneficial interactions with commensal and symbiotic microbes. One of the major convergent points for plant immune signaling is the nucleus, where transcriptome reprogramming is initiated to orchestrate defense responses. Mechanisms that regulate selective transport of nuclear signaling cargo and chromatin activity at the nuclear boundary play a pivotal role in immune activation. This review summarizes the current knowledge of how nuclear membrane-associated core protein and protein complexes, including the nuclear pore complex, nuclear transport receptors, and the nucleoskeleton participate in plant innate immune activation and pathogen resistance. We also discuss the role of their functional counterparts in regulating innate immunity in animals and highlight potential common mechanisms that contribute to nuclear membrane-centered immune regulation in higher eukaryotes.
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Affiliation(s)
- Yiling Fang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States.,Innovative Genomics Institute, University of California, Berkeley, CA, United States
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States.,Innovative Genomics Institute, University of California, Berkeley, CA, United States
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10
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Cai YD, Chiu JC. Timeless in animal circadian clocks and beyond. FEBS J 2021; 289:6559-6575. [PMID: 34699674 PMCID: PMC9038958 DOI: 10.1111/febs.16253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/09/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
TIMELESS (TIM) was first identified as a molecular cog in the Drosophila circadian clock. Almost three decades of investigations have resulted in an insightful model describing the critical role of Drosophila TIM (dTIM) in circadian timekeeping in insects, including its function in mediating light entrainment and temperature compensation of the molecular clock. Furthermore, exciting discoveries on its sequence polymorphism and thermosensitive alternative RNA splicing have also established its role in regulating seasonal biology. Although mammalian TIM (mTIM), its mammalian paralog, was first identified as a potential circadian clock component in 1990s due to sequence similarity to dTIM, its role in clock regulation has been more controversial. Mammalian TIM has now been characterized as a DNA replication fork component and has been shown to promote fork progression and participate in cell cycle checkpoint signaling in response to DNA damage. Despite defective circadian rhythms displayed by mtim mutants, it remains controversial whether the regulation of circadian clocks by mTIM is direct, especially given the interconnection between the cell cycle and circadian clocks. In this review, we provide a historical perspective on the identification of animal tim genes, summarize the roles of TIM proteins in biological timing and genomic stability, and draw parallels between dTIM and mTIM despite apparent functional divergence.
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Affiliation(s)
- Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
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11
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Xing X, Gu F, Hua L, Cui X, Li D, Wu Z, Zhang R. TIMELESS Promotes Tumor Progression by Enhancing Macrophages Recruitment in Ovarian Cancer. Front Oncol 2021; 11:732058. [PMID: 34490127 PMCID: PMC8417241 DOI: 10.3389/fonc.2021.732058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/29/2021] [Indexed: 01/11/2023] Open
Abstract
Objective Ovarian cancer (OV) is the most fatal and frequent type of gynecological malignancy worldwide. TIMELESS (TIM), as a circadian clock gene, has been found to be highly expressed and predictive of poor prognosis in various cancers. However, the function of TIM in OV is not known. This study was designed to investigate the biological functions and underlying mechanisms of TIM during OV progression. Methods Cell viability assay, cell migration assay, immunohistochemistry staining, qPCR analyses, and tumor xenograft model were used to identify the functions of TIM in OV. Bioinformatics analyses, including GEPIA, cBioPortal, GeneMANIA, and TIMER, were used to analyze the gene expression, genetic alteration, and immune cell infiltration of TIM in OV. Results TIM is highly expressed in OV patients. TIM knockdown inhibited OV cell proliferation, migration, and invasion both in vitro and in vivo. Genetic alteration of TIM was identified in patients with OV. TIM co-expression network indicates that TIM had a wide effect on the immune cell infiltration and activation in OV. Further analysis and experimental verification revealed that TIM was positively correlated with macrophages infiltration in OV. Conclusions Our study unveiled a novel function of highly expressed TIM associated with immune cell especially macrophages infiltration in OV. TIM may serve as a potential prognostic biomarker and immunotherapy target for OV patients.
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Affiliation(s)
- Xin Xing
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Fei Gu
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Lanyu Hua
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoxiao Cui
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Dongxue Li
- Shanghai Cancer Institute, Shanghai, China
| | - Zhiyong Wu
- Gynecology Department, Shanghai Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
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12
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Chen GQ, Li P, Yan Q, Wu YH, Wang HR, Chao SF, Wu LJ, Chen L, Feng GZ. Identification of Spodoptera frugiperda importin alphas that facilitate the nuclear import of Autographa californica multiple nucleopolyhedrovirus DNA polymerase. INSECT MOLECULAR BIOLOGY 2021; 30:400-409. [PMID: 33837597 DOI: 10.1111/imb.12704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Proteins containing nuclear localization signals (NLSs) are actively transported into the nucleus via the classic importin-α/β-mediated pathway, and NLSs are recognized by members of the importin-α family. Most studies of insect importin-αs have focused on Drosophila to date, little is known about the importin-α proteins in Lepidoptera insects. In this study, we identified four putative importin-α homologues, Spodoptera frugiperda importin-α1 (SfIMA1), SfIMA2, SfIMA4 and SfIMA7, from Sf9 cells. Immunofluorescence analysis showed that SfIMA2, SfIMA4 and SfIMA7 localized to the nucleus, while SfIMA1 distributed in cytoplasm. Additionally, SfIMA4 and SfIMA7 were also detected in the nuclear membrane of Sf9 cells. SfIMA1, SfIMA4 and SfIMA7, but not SfIMA2, were found to associate with the C terminus of AcMNPV DNA polymerase (DNApol) that harbours a typical monopartite NLS and a classic bipartite NLS. Further analysis of protein-protein interactions revealed that SfIMA1 specifically recognizes the bipartite NLS, while SfIMA4 and SfIMA7 bind to both monopartite and bipartite NLSs. Together, our results suggested that SfIMA1, SfIMA4 and SfIMA7 play important roles in the nuclear import of AcMNPV DNApol C terminus in Sf9 cells.
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Affiliation(s)
- Guo-Qing Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Pei Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Qing Yan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yi-Hong Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Hao-Ran Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shu-Fen Chao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li-Juan Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Long Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guo-Zhong Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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13
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Cao M, Wang Y, Xiao Y, Zheng D, Zhi C, Xia X, Yuan X. Activation of the clock gene TIMELESS by H3k27 acetylation promotes colorectal cancer tumorigenesis by binding to Myosin-9. J Exp Clin Cancer Res 2021; 40:162. [PMID: 33971927 PMCID: PMC8108341 DOI: 10.1186/s13046-021-01936-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 04/03/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a common tumor characterized by its high mortality. However, the underlying molecular mechanisms that drive CRC tumorigenesis are unclear. Clock genes have important roles in tumor development. In the present study, the expression and functions of clock gene TIMELESS (encoding the Timeless protein) in CRC were investigated. METHODS Immunohistochemistry, cell proliferation, migration, invasion, EMT and xenograft tumor experiments were used to prove the function of Timeless in the tumorigenesis of CRC. Immunoprecipitation, mass spectrometry, Immunofluorescence and Chromatin immunoprecipitation (ChIP) were utilized to clarify the mechanism of Timeless in regulating CRC tumorigenesis. RESULTS We found that Timeless was upregulated in CRC tissues compared with corresponding normal tissues and its expression was closely associated with the TNM stages and overall survival of CRC patients. Functional studies demonstrated that Timeless promoted the proliferation, invasion, and EMT of CRC cells in vitro and in vivo. Mechanistic investigations showed that Timeless activated the β-catenin signal pathway by binding to Myosin-9, which binds to β-catenin to induce its nuclear translocation. The upregulation of Timeless was attributed to CREB-binding protein (CBP)/p300-mediated H3K27 acetylation of the promoter region of Timeless. CONCLUSION Timeless regulates the tumorigenesis of CRC by binding to and regulating myosin-9, suggesting Timeless might be a potential prognostic biomarker and therapeutic target for CRC.
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Affiliation(s)
- Meng Cao
- Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Yi Wang
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Yijing Xiao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, China
| | - Dandan Zheng
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Chunchun Zhi
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Xin Xia
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Xiaoqin Yuan
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China.
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing, 211166, China.
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14
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Rosbash M. Circadian Rhythms and the Transcriptional Feedback Loop (Nobel Lecture)**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Rosbash
- Department of Biology Howard Hughes Medical Institute Brandeis University Waltham MA USA
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15
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Rosbash M. Circadian Rhythms and the Transcriptional Feedback Loop (Nobel Lecture)**. Angew Chem Int Ed Engl 2021; 60:8650-8666. [DOI: 10.1002/anie.202015199] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Rosbash
- Department of Biology Howard Hughes Medical Institute Brandeis University Waltham MA USA
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16
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Cai YD, Xue Y, Truong CC, Del Carmen-Li J, Ochoa C, Vanselow JT, Murphy KA, Li YH, Liu X, Kunimoto BL, Zheng H, Zhao C, Zhang Y, Schlosser A, Chiu JC. CK2 Inhibits TIMELESS Nuclear Export and Modulates CLOCK Transcriptional Activity to Regulate Circadian Rhythms. Curr Biol 2021; 31:502-514.e7. [PMID: 33217322 PMCID: PMC7878342 DOI: 10.1016/j.cub.2020.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 11/06/2022]
Abstract
Circadian clocks orchestrate daily rhythms in organismal physiology and behavior to promote optimal performance and fitness. In Drosophila, key pacemaker proteins PERIOD (PER) and TIMELESS (TIM) are progressively phosphorylated to perform phase-specific functions. Whereas PER phosphorylation has been extensively studied, systematic analysis of site-specific TIM phosphorylation is lacking. Here, we identified phosphorylation sites of PER-bound TIM by mass spectrometry, given the importance of TIM as a modulator of PER function in the pacemaker. Among the 12 TIM phosphorylation sites we identified, at least two of them are critical for circadian timekeeping as mutants expressing non-phosphorylatable mutations exhibit altered behavioral rhythms. In particular, we observed that CK2-dependent phosphorylation of TIM(S1404) promotes nuclear accumulation of PER-TIM heterodimers by inhibiting the interaction of TIM and nuclear export component, Exportin 1 (XPO1). We propose that proper level of nuclear PER-TIM accumulation is necessary to facilitate kinase recruitment for the regulation of daily phosphorylation rhythm and phase-specific transcriptional activity of CLOCK (CLK). Our results highlight the contribution of phosphorylation-dependent nuclear export of PER-TIM heterodimers to the maintenance of circadian periodicity and identify a new mechanism by which the negative elements of the circadian clock (PER-TIM) regulate the positive elements (CLK-CYC). Finally, because the molecular phenotype of tim(S1404A) non-phosphorylatable mutant exhibits remarkable similarity to that of a mutation in human timeless that underlies familial advanced sleep phase syndrome (FASPS), our results revealed an unexpected parallel between the functions of Drosophila and human TIM and may provide new insights into the molecular mechanisms underlying human FASPS. Organisms in all domains of life exhibit circadian rhythms. Cai et al. reveal that phosphorylation of TIMELESS modulates kinase accessibility to CLOCK in the nucleus. This mechanism is important in controlling daily phosphorylation rhythm of CLOCK, which is critical for its function as a key regulator of circadian rhythms.
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Affiliation(s)
- Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Yongbo Xue
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Cindy C Truong
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jose Del Carmen-Li
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher Ochoa
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Wurzburg, Wurzburg, Germany
| | - Katherine A Murphy
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ying H Li
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ben L Kunimoto
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Wurzburg, Wurzburg, Germany
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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17
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Misregulation of Drosophila Myc Disrupts Circadian Behavior and Metabolism. Cell Rep 2020; 29:1778-1788.e4. [PMID: 31722196 PMCID: PMC6910219 DOI: 10.1016/j.celrep.2019.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/29/2019] [Accepted: 10/04/2019] [Indexed: 11/20/2022] Open
Abstract
Drosophila Myc (dMyc) is highly conserved and functions as a transcription factor similar to mammalian Myc. We previously found that oncogenic Myc disrupts the molecular clock in cancer cells. Here, we demonstrate that misregulation of dMyc expression affects Drosophila circadian behavior. dMyc overexpression results in a high percentage of arrhythmic flies, concomitant with increases in the expression of clock genes cyc, tim, cry, and cwo. Conversely, flies with hypomorphic mutations in dMyc exhibit considerable arrhythmia, which can be rescued by loss of dMnt, a suppressor of dMyc activity. Metabolic profiling of fly heads revealed that loss of dMyc and its overexpression alter steady-state metabolite levels and have opposing effects on histidine, the histamine precursor, which is rescued in dMyc mutants by ablation of dMnt and could contribute to effects of dMyc on locomotor behavior. Our results demonstrate a role of dMyc in modulating Drosophila circadian clock, behavior, and metabolism.
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18
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Chakraborty A, Aziz F, Roh E, Le LTM, Dey R, Zhang T, Rathore MG, Biswas AS, Bode AM, Dong Z. Knock-down of the TIM/TIPIN complex promotes apoptosis in melanoma cells. Oncotarget 2020; 11:1846-1861. [PMID: 32499870 PMCID: PMC7244016 DOI: 10.18632/oncotarget.27572] [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: 01/30/2020] [Accepted: 04/10/2020] [Indexed: 11/25/2022] Open
Abstract
The Timeless (TIM) and it's interacting partner TIPIN protein complex is well known for its role in replication checkpoints and normal DNA replication processes. Recent studies revealed the involvement of TIM and TIPIN in human malignancies; however, no evidence is available regarding the expression of the TIM/TIPIN protein complex or its potential role in melanoma. Therefore, we investigated the role of this complex in melanoma. To assess the role of the TIM/TIPIN complex in melanoma, we analyzed TIM/TIPIN expression data from the publicly accessible TCGA online database, Western blot analysis, and RT-qPCR in a panel of melanoma cell lines. Lentivirus-mediated TIM/TIPIN knockdown in A375 melanoma cells was used to examine proliferation, colony formation, and apoptosis. A xenograft tumor formation assay was also performed. The TIM/TIPIN complex is frequently overexpressed in melanoma cells compared to normal melanocytes. We also discovered that the overexpression of TIM and TIPIN was significantly associated with poorer prognosis of melanoma patients. Furthermore, we observed that shRNA-mediated knockdown of TIM and TIPIN reduced cell viability and proliferation due to the induction of apoptosis and increased levels of γH2AX, a marker of DNA damage. In a xenograft tumor nude mouse model, shRNA-knockdown of TIM/TIPIN significantly reduced tumor growth. Our results suggest that the TIM/TIPIN complex plays an important role in tumorigenesis of melanoma, which might reveal novel approaches for the development of new melanoma therapies. Our studies also provide a beginning structural basis for understanding the assembly of the TIM/TIPIN complex. Further mechanistic investigations are needed to determine the complex’s potential as a biomarker of melanoma susceptibility. Targeting TIM/TIPIN might be a potential therapeutic strategy against melanoma.
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Affiliation(s)
- Abhijit Chakraborty
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Immunology, Allergy and Rheumatology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Faisal Aziz
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Eunmiri Roh
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Le Thi My Le
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Raja Dey
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Moeez G Rathore
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Aalekhya Sharma Biswas
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Pediatric Gastroenterology and Liver Center, Baylor College of Medicine, Houston, Texas, Houston, TX 77030, USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,College of Medicine, Zhengzhou University, Zhengzhou, Henan Province 450052, China
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19
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Yao X, Kojima S, Chen J. Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. PLoS Comput Biol 2020; 16:e1007842. [PMID: 32339166 PMCID: PMC7205317 DOI: 10.1371/journal.pcbi.1007842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/07/2020] [Accepted: 04/02/2020] [Indexed: 11/18/2022] Open
Abstract
The mammalian circadian clock is deeply rooted in rhythmic regulation of gene expression. Rhythmic transcriptional control mediated by the circadian transcription factors is thought to be the main driver of mammalian circadian gene expression. However, mounting evidence has demonstrated the importance of rhythmic post-transcriptional controls, and it remains unclear how the transcriptional and post-transcriptional mechanisms collectively control rhythmic gene expression. In mouse liver, hundreds of genes were found to exhibit rhythmicity in poly(A) tail length, and the poly(A) rhythms are strongly correlated with the protein expression rhythms. To understand the role of rhythmic poly(A) regulation in circadian gene expression, we constructed a parsimonious model that depicts rhythmic control imposed upon basic mRNA expression and poly(A) regulation processes, including transcription, deadenylation, polyadenylation, and degradation. The model results reveal the rhythmicity in deadenylation as the strongest contributor to the rhythmicity in poly(A) tail length and the rhythmicity in the abundance of the mRNA subpopulation with long poly(A) tails (a rough proxy for mRNA translatability). In line with this finding, the model further shows that the experimentally observed distinct peak phases in the expression of deadenylases, regardless of other rhythmic controls, can robustly cluster the rhythmic mRNAs by their peak phases in poly(A) tail length and abundance of the long-tailed subpopulation. This provides a potential mechanism to synchronize the phases of target gene expression regulated by the same deadenylases. Our findings highlight the critical role of rhythmic deadenylation in regulating poly(A) rhythms and circadian gene expression.
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Affiliation(s)
- Xiangyu Yao
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Genetics, Bioinformatics, and Computational Biology program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Shihoko Kojima
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
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20
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Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington's Disease. Cancers (Basel) 2020; 12:cancers12040963. [PMID: 32295075 PMCID: PMC7226183 DOI: 10.3390/cancers12040963] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence points to a link between circadian clock dysfunction and the molecular events that drive tumorigenesis. Here, we investigated the connection between the circadian clock and the hallmarks of cancer in an in vitro model of colorectal cancer (CRC). We used a cross-platform data normalization method to concatenate and compare available microarray and RNA-sequencing time series data of CRC cell lines derived from the same patient at different disease stages. Our data analysis suggests differential regulation of molecular pathways between the CRC cells and identifies several of the circadian and likely clock-controlled genes (CCGs) as cancer hallmarks and circadian drug targets. Notably, we found links of the CCGs to Huntington’s disease (HD) in the metastasis-derived cells. We then investigated the impact of perturbations of our candidate genes in a cohort of 439 patients with colon adenocarcinoma retrieved from the Cancer Genome Atlas (TCGA). The analysis revealed a correlation of the differential expression levels of the candidate genes with the survival of patients. Thus, our study provides a bioinformatics workflow that allows for a comprehensive analysis of circadian properties at different stages of colorectal cancer, and identifies a new association between cancer and HD.
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21
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Serway CN, Dunkelberger BS, Del Padre D, Nolan NWC, Georges S, Freer S, Andres AJ, de Belle JS. Importin-α2 mediates brain development, learning and memory consolidation in Drosophila. J Neurogenet 2020; 34:69-82. [PMID: 31965871 DOI: 10.1080/01677063.2019.1709184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Neuronal development and memory consolidation are conserved processes that rely on nuclear-cytoplasmic transport of signaling molecules to regulate gene activity and initiate cascades of downstream cellular events. Surprisingly, few reports address and validate this widely accepted perspective. Here we show that Importin-α2 (Imp-α2), a soluble nuclear transporter that shuttles cargoes between the cytoplasm and nucleus, is vital for brain development, learning and persistent memory in Drosophila melanogaster. Mutations in importin-α2 (imp-α2, known as Pendulin or Pen and homologous with human KPNA2) are alleles of mushroom body miniature B (mbmB), a gene known to regulate aspects of brain development and influence adult behavior in flies. Mushroom bodies (MBs), paired associative centers in the brain, are smaller than normal due to defective proliferation of specific intrinsic Kenyon cell (KC) neurons in mbmB mutants. Extant KCs projecting to the MB β-lobe terminate abnormally on the contralateral side of the brain. mbmB adults have impaired olfactory learning but normal memory decay in most respects, except that protein synthesis-dependent long-term memory (LTM) is abolished. This observation supports an alternative mechanism of persistent memory in which mutually exclusive protein-synthesis-dependent and -independent forms rely on opposing cellular mechanisms or circuits. We propose a testable model of Imp-α2 and nuclear transport roles in brain development and conditioned behavior. Based on our molecular characterization, we suggest that mbmB is hereafter referred to as imp-α2mbmB.
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Affiliation(s)
- Christine N Serway
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.,Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Brian S Dunkelberger
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.,Las Vegas High School, Las Vegas, NV, USA
| | - Denise Del Padre
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Nicole W C Nolan
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.,Methodist Estabrook Cancer Center, Omaha, NE, USA
| | - Stephanie Georges
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.,Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Stephanie Freer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.,Research Square Inc, Nashville, TN, USA
| | - Andrew J Andres
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - J Steven de Belle
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.,Department of Psychological Sciences, University of San Diego, San Diego, CA, USA
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22
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Singh S, Giesecke A, Damulewicz M, Fexova S, Mazzotta GM, Stanewsky R, Dolezel D. New Drosophila Circadian Clock Mutants Affecting Temperature Compensation Induced by Targeted Mutagenesis of Timeless. Front Physiol 2019; 10:1442. [PMID: 31849700 PMCID: PMC6901700 DOI: 10.3389/fphys.2019.01442] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022] Open
Abstract
Drosophila melanogaster has served as an excellent genetic model to decipher the molecular basis of the circadian clock. Two key proteins, PERIOD (PER) and TIMELESS (TIM), are particularly well explored and a number of various arrhythmic, slow, and fast clock mutants have been identified in classical genetic screens. Interestingly, the free running period (tau, τ) is influenced by temperature in some of these mutants, whereas τ is temperature-independent in other mutant lines as in wild-type flies. This, so-called "temperature compensation" ability is compromised in the mutant timeless allele "ritsu" (tim rit ), and, as we show here, also in the tim blind allele, mapping to the same region of TIM. To test if this region of TIM is indeed important for temperature compensation, we generated a collection of new mutants and mapped functional protein domains involved in the regulation of τ and in general clock function. We developed a protocol for targeted mutagenesis of specific gene regions utilizing the CRISPR/Cas9 technology, followed by behavioral screening. In this pilot study, we identified 20 new timeless mutant alleles with various impairments of temperature compensation. Molecular characterization revealed that the mutations included short in-frame insertions, deletions, or substitutions of a few amino acids resulting from the non-homologous end joining repair process. Our protocol is a fast and cost-efficient systematic approach for functional analysis of protein-coding genes and promoter analysis in vivo. Interestingly, several mutations with a strong temperature compensation defect map to one specific region of TIM. Although the exact mechanism of how these mutations affect TIM function is as yet unknown, our in silico analysis suggests they affect a putative nuclear export signal (NES) and phosphorylation sites of TIM. Immunostaining for PER was performed on two TIM mutants that display longer τ at 25°C and complete arrhythmicity at 28°C. Consistently with the behavioral phenotype, PER immunoreactivity was reduced in circadian clock neurons of flies exposed to elevated temperatures.
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Affiliation(s)
- Samarjeet Singh
- Institute of Entomology, Biology Centre of Academy of Sciences of the Czech Republic, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Astrid Giesecke
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Milena Damulewicz
- Institute of Entomology, Biology Centre of Academy of Sciences of the Czech Republic, České Budějovice, Czechia
- Department of Cell Biology and Imaging, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - Silvie Fexova
- Institute of Entomology, Biology Centre of Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Gabriella M. Mazzotta
- Institute of Entomology, Biology Centre of Academy of Sciences of the Czech Republic, České Budějovice, Czechia
- Department of Biology, University of Padua, Padua, Italy
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - David Dolezel
- Institute of Entomology, Biology Centre of Academy of Sciences of the Czech Republic, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
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23
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Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle. Cell Rep 2019; 23:2273-2282. [PMID: 29791839 DOI: 10.1016/j.celrep.2018.04.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/10/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022] Open
Abstract
Circadian clocks have evolved as time-measuring molecular devices to help organisms adapt their physiology to daily changes in light and temperature. Transcriptional oscillations account for a large fraction of rhythmic protein abundance. However, cycling of various posttranslational modifications, such as ubiquitylation, also contributes to shape the rhythmic protein landscape. In this study, we used an in vivo ubiquitin labeling assay to investigate the circadian ubiquitylated proteome of Drosophila melanogaster. We find that cyclic ubiquitylation affects MEGATOR (MTOR), a chromatin-associated nucleoporin that, in turn, feeds back to regulate the core molecular oscillator. Furthermore, we show that the ubiquitin ligase subunits CULLIN-3 (CUL-3) and SUPERNUMERARY LIMBS (SLMB) cooperate for ubiquitylating the TIMELESS protein. These findings stress the importance of ubiquitylation pathways in the Drosophila circadian clock and reveal a key component of this system.
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24
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Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol 2019; 21:67-84. [PMID: 31768006 DOI: 10.1038/s41580-019-0179-2] [Citation(s) in RCA: 549] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
To accommodate daily recurring environmental changes, animals show cyclic variations in behaviour and physiology, which include prominent behavioural states such as sleep-wake cycles but also a host of less conspicuous oscillations in neurological, metabolic, endocrine, cardiovascular and immune functions. Circadian rhythmicity is created endogenously by genetically encoded molecular clocks, whose components cooperate to generate cyclic changes in their own abundance and activity, with a periodicity of about a day. Throughout the body, such molecular clocks convey temporal control to the function of organs and tissues by regulating pertinent downstream programmes. Synchrony between the different circadian oscillators and resonance with the solar day is largely enabled by a neural pacemaker, which is directly responsive to certain environmental cues and able to transmit internal time-of-day representations to the entire body. In this Review, we discuss aspects of the circadian clock in Drosophila melanogaster and mammals, including the components of these molecular oscillators, the function and mechanisms of action of central and peripheral clocks, their synchronization and their relevance to human health.
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25
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Arnes M, Alaniz ME, Karam CS, Cho JD, Lopez G, Javitch JA, Santa-Maria I. Role of Tau Protein in Remodeling of Circadian Neuronal Circuits and Sleep. Front Aging Neurosci 2019; 11:320. [PMID: 31824299 PMCID: PMC6881280 DOI: 10.3389/fnagi.2019.00320] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/04/2019] [Indexed: 01/08/2023] Open
Abstract
Multiple neurological, physiological, and behavioral functions are synchronized by circadian clocks into daily rhythms. Neurodegenerative diseases such as Alzheimer's disease and related tauopathies are associated with a decay of circadian rhythms, disruption of sleep patterns, and impaired cognitive function but the mechanisms underlying these alterations are still unclear. Traditional approaches in neurodegeneration research have focused on understanding how pathology impinges on circadian function. Since in Alzheimer's disease and related tauopathies tau proteostasis is compromised, here we sought to understand the role of tau protein in neuronal circadian biology and related behavior. Considering molecular mechanisms underlying circadian rhythms are conserved from Drosophila to humans, here we took advantage of a recently developed tau-deficient Drosophila line to show that loss of tau promotes dysregulation of daily circadian rhythms and sleep patterns. Strikingly, tau deficiency dysregulates the structural plasticity of the small ventral lateral circadian pacemaker neurons by disrupting the temporal cytoskeletal remodeling of its dorsal axonal projections and by inducing a slight increase in the cytoplasmic accumulation of core clock proteins. Taken together, these results suggest that loss of tau function participates in the regulation of circadian rhythms by modulating the correct operation and connectivity of core circadian networks and related behavior.
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Affiliation(s)
- Mercedes Arnes
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Maria E. Alaniz
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Caline S. Karam
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Joshua D. Cho
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jonathan A. Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
- Department of Pharmacology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Ismael Santa-Maria
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
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26
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Hunt LC, Jiao J, Wang YD, Finkelstein D, Rao D, Curley M, Robles-Murguia M, Shirinifard A, Pagala VR, Peng J, Fan Y, Demontis F. Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations. Genome Res 2019; 29:1262-1276. [PMID: 31249065 PMCID: PMC6673717 DOI: 10.1101/gr.246884.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/25/2019] [Indexed: 12/17/2022]
Abstract
Organisms use endogenous clocks to adapt to the rhythmicity of the environment and to synchronize social activities. Although the circadian cycle is implicated in aging, it is unknown whether natural variation in its function contributes to differences in lifespan between populations and whether the circadian clock of specific tissues is key for longevity. We have sequenced the genomes of Drosophila melanogaster strains with exceptional longevity that were obtained via multiple rounds of selection from a parental strain. Comparison of genomic, transcriptomic, and proteomic data revealed that changes in gene expression due to intergenic polymorphisms are associated with longevity and preservation of skeletal muscle function with aging in these strains. Analysis of transcription factors differentially modulated in long-lived versus parental strains indicates a possible role of circadian clock core components. Specifically, there is higher period and timeless and lower cycle expression in the muscle of strains with delayed aging compared to the parental strain. These changes in the levels of circadian clock transcription factors lead to changes in the muscle circadian transcriptome, which includes genes involved in metabolism, proteolysis, and xenobiotic detoxification. Moreover, a skeletal muscle-specific increase in timeless expression extends lifespan and recapitulates some of the transcriptional and circadian changes that differentiate the long-lived from the parental strains. Altogether, these findings indicate that the muscle circadian clock is important for longevity and that circadian gene variants contribute to the evolutionary divergence in longevity across populations.
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Affiliation(s)
- Liam C Hunt
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jianqin Jiao
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Deepti Rao
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Michelle Curley
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Maricela Robles-Murguia
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Vishwajeeth R Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.,Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Fabio Demontis
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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27
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PERIOD-controlled deadenylation of the timeless transcript in the Drosophila circadian clock. Proc Natl Acad Sci U S A 2019; 116:5721-5726. [PMID: 30833404 DOI: 10.1073/pnas.1814418116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The Drosophila circadian oscillator relies on a negative transcriptional feedback loop, in which the PERIOD (PER) and TIMELESS (TIM) proteins repress the expression of their own gene by inhibiting the activity of the CLOCK (CLK) and CYCLE (CYC) transcription factors. A series of posttranslational modifications contribute to the oscillations of the PER and TIM proteins but few posttranscriptional mechanisms have been described that affect mRNA stability. Here we report that down-regulation of the POP2 deadenylase, a key component of the CCR4-NOT deadenylation complex, alters behavioral rhythms. Down-regulating POP2 specifically increases TIM protein and tim mRNA but not tim pre-mRNA, supporting a posttranscriptional role. Indeed, reduced POP2 levels induce a lengthening of tim mRNA poly(A) tail. Surprisingly, such effects are lost in per 0 mutants, supporting a PER-dependent inhibition of tim mRNA deadenylation by POP2. We report a deadenylation mechanism that controls the oscillations of a core clock gene transcript.
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28
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Li YH, Liu X, Vanselow JT, Zheng H, Schlosser A, Chiu JC. O-GlcNAcylation of PERIOD regulates its interaction with CLOCK and timing of circadian transcriptional repression. PLoS Genet 2019; 15:e1007953. [PMID: 30703153 PMCID: PMC6372208 DOI: 10.1371/journal.pgen.1007953] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/12/2019] [Accepted: 01/10/2019] [Indexed: 11/18/2022] Open
Abstract
Circadian clocks coordinate time-of-day-specific metabolic and physiological processes to maximize organismal performance and fitness. In addition to light and temperature, which are regarded as strong zeitgebers for circadian clock entrainment, metabolic input has now emerged as an important signal for clock entrainment and modulation. Circadian clock proteins have been identified to be substrates of O-GlcNAcylation, a nutrient sensitive post-translational modification (PTM), and the interplay between clock protein O-GlcNAcylation and other PTMs is now recognized as an important mechanism by which metabolic input regulates circadian physiology. To better understand the role of O-GlcNAcylation in modulating clock protein function within the molecular oscillator, we used mass spectrometry proteomics to identify O-GlcNAcylation sites of PERIOD (PER), a repressor of the circadian transcriptome and a critical biochemical timer of the Drosophila clock. In vivo functional characterization of PER O-GlcNAcylation sites indicates that O-GlcNAcylation at PER(S942) reduces interactions between PER and CLOCK (CLK), the key transcriptional activator of clock-controlled genes. Since we observe a correlation between clock-controlled daytime feeding activity and higher level of PER O-GlcNAcylation, we propose that PER(S942) O-GlcNAcylation during the day functions to prevent premature initiation of circadian repression phase. This is consistent with the period-shortening behavioral phenotype of per(S942A) flies. Taken together, our results support that clock-controlled feeding activity provides metabolic signals to reinforce light entrainment to regulate circadian physiology at the post-translational level. The interplay between O-GlcNAcylation and other PTMs to regulate circadian physiology is expected to be complex and extensive, and reach far beyond the molecular oscillator.
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Affiliation(s)
- Ying H. Li
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States of America
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States of America
| | - Jens T. Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ, United States of America
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States of America
- * E-mail:
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29
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Shakhmantsir I, Nayak S, Grant GR, Sehgal A. Spliceosome factors target timeless ( tim) mRNA to control clock protein accumulation and circadian behavior in Drosophila. eLife 2018; 7:39821. [PMID: 30516472 PMCID: PMC6281371 DOI: 10.7554/elife.39821] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022] Open
Abstract
Transcription-translation feedback loops that comprise eukaryotic circadian clocks rely upon temporal delays that separate the phase of active transcription of clock genes, such as Drosophila period (per) and timeless (tim), from negative feedback by the two proteins. However, our understanding of the mechanisms involved is incomplete. Through an RNA interference screen, we found that pre-mRNA processing 4 (PRP4) kinase, a component of the U4/U5.U6 triple small nuclear ribonucleoprotein (tri-snRNP) spliceosome, and other tri-snRNP components regulate cycling of the molecular clock as well as rest:activity rhythms. Unbiased RNA-Sequencing uncovered an alternatively spliced intron in tim whose increased retention upon prp4 downregulation leads to decreased TIM levels. We demonstrate that the splicing of tim is rhythmic with a phase that parallels delayed accumulation of the protein in a 24 hr cycle. We propose that alternative splicing constitutes an important clock mechanism for delaying the daily accumulation of clock proteins, and thereby negative feedback by them. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Iryna Shakhmantsir
- Chronobiology Program at Penn, Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Soumyashant Nayak
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Gregory R Grant
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Amita Sehgal
- Chronobiology Program at Penn, Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
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30
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Kosyna FK, Depping R. Controlling the Gatekeeper: Therapeutic Targeting of Nuclear Transport. Cells 2018; 7:cells7110221. [PMID: 30469340 PMCID: PMC6262578 DOI: 10.3390/cells7110221] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022] Open
Abstract
Nuclear transport receptors of the karyopherin superfamily of proteins transport macromolecules from one compartment to the other and are critical for both cell physiology and pathophysiology. The nuclear transport machinery is tightly regulated and essential to a number of key cellular processes since the spatiotemporally expression of many proteins and the nuclear transporters themselves is crucial for cellular activities. Dysregulation of the nuclear transport machinery results in localization shifts of specific cargo proteins and associates with the pathogenesis of disease states such as cancer, inflammation, viral illness and neurodegenerative diseases. Therefore, inhibition of the nuclear transport system has future potential for therapeutic intervention and could contribute to the elucidation of disease mechanisms. In this review, we recapitulate clue findings in the pathophysiological significance of nuclear transport processes and describe the development of nuclear transport inhibitors. Finally, clinical implications and results of the first clinical trials are discussed for the most promising nuclear transport inhibitors.
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Affiliation(s)
- Friederike K Kosyna
- Institute of Physiology, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.
| | - Reinhard Depping
- Institute of Physiology, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.
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31
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CK1α Collaborates with DOUBLETIME to Regulate PERIOD Function in the Drosophila Circadian Clock. J Neurosci 2018; 38:10631-10643. [PMID: 30373768 DOI: 10.1523/jneurosci.0871-18.2018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/05/2018] [Accepted: 10/21/2018] [Indexed: 11/21/2022] Open
Abstract
The animal circadian timing system interprets environmental time cues and internal metabolic status to orchestrate circadian rhythms of physiology, allowing animals to perform necessary tasks in a time-of-day-dependent manner. Normal progression of circadian rhythms is dependent on the daily cycling of core transcriptional factors that make up cell-autonomous molecular oscillators. In Drosophila, PERIOD (PER), TIMELESS (TIM), CLOCK (CLK), and CYCLE (CYC) are core clock proteins that function in a transcriptional-translational feedback mechanism to regulate the circadian transcriptome. Posttranslational modifications of core clock proteins provide precise temporal control over when they are active as regulators of clock-controlled genes. In particular, phosphorylation is a key regulatory mechanism that dictates the subcellular localization, stability, and transcriptional activity of clock proteins. Previously, casein kinase 1α (CK1α) has been identified as a kinase that phosphorylates mammalian PER1 and modulates its stability, but the mechanisms by which it modulates PER protein stability is still unclear. Using Drosophila as a model, we show that CK1α has an overall function of speeding up PER metabolism and is required to maintain the 24 h period of circadian rhythms. Our results indicate that CK1α collaborates with the key clock kinase DOUBLETIME (DBT) in both the cytoplasm and the nucleus to regulate the timing of PER-dependent repression of the circadian transcriptome. Specifically, we observe that CK1α promotes PER nuclear localization by antagonizing the activity of DBT to inhibit PER nuclear translocation. Furthermore, CK1α enhances DBT-dependent PER phosphorylation and degradation once PER moves into the nucleus.SIGNIFICANCE STATEMENT Circadian clocks are endogenous timers that integrate environmental signals to impose temporal control over organismal physiology over the 24 h day/night cycle. To maintain the 24 h period length of circadian clocks and to ensure that circadian rhythms are in synchrony with the external environment, key proteins that make up the molecular oscillator are extensively regulated by phosphorylation to ensure that they perform proper time-of-day-specific functions. Casein kinase 1α (CK1α) has previously been identified as a kinase that phosphorylates mammalian PERIOD (PER) proteins to promote their degradation, but the mechanism by which it modulates PER stability is unclear. In this study, we characterize the mechanisms by which CK1α interacts with DOUBLETIME (DBT) to achieve the overall function of speeding up PER metabolism and to ensure proper time-keeping.
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32
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Young MW. Reise durch die Zeit: 40 Jahre Forschung von den Clock-Mutanten in Drosophila zu Störungen des zirkadianen Rhythmus beim Menschen (Nobel-Vortrag). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michael W. Young
- Laboratory of Genetics; The Rockefeller University; 1230 York Avenue New York NY 10065 USA
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33
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Young MW. Time Travels: A 40‐Year Journey from Drosophila's Clock Mutants to Human Circadian Disorders (Nobel Lecture). Angew Chem Int Ed Engl 2018; 57:11532-11539. [DOI: 10.1002/anie.201803337] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Michael W. Young
- Laboratory of GeneticsThe Rockefeller University 1230 York Avenue New York NY 10065 USA
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34
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Beck K, Hovhanyan A, Menegazzi P, Helfrich-Förster C, Raabe T. Drosophila RSK Influences the Pace of the Circadian Clock by Negative Regulation of Protein Kinase Shaggy Activity. Front Mol Neurosci 2018; 11:122. [PMID: 29706866 PMCID: PMC5908959 DOI: 10.3389/fnmol.2018.00122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/28/2018] [Indexed: 11/18/2022] Open
Abstract
Endogenous molecular circadian clocks drive daily rhythmic changes at the cellular, physiological, and behavioral level for adaptation to and anticipation of environmental signals. The core molecular system consists of autoregulatory feedback loops, where clock proteins inhibit their own transcription. A complex and not fully understood interplay of regulatory proteins influences activity, localization and stability of clock proteins to set the pace of the clock. This study focuses on the molecular function of Ribosomal S6 Kinase (RSK) in the Drosophila melanogaster circadian clock. Mutations in the human rsk2 gene cause Coffin–Lowry syndrome, which is associated with severe mental disabilities. Knock-out studies with Drosophila ortholog rsk uncovered functions in synaptic processes, axonal transport and adult behavior including associative learning and circadian activity. However, the molecular targets of RSK remain elusive. Our experiments provide evidence that RSK acts in the key pace maker neurons as a negative regulator of Shaggy (SGG) kinase activity, which in turn determines timely nuclear entry of the clock proteins Period and Timeless to close the negative feedback loop. Phosphorylation of serine 9 in SGG is mediated by the C-terminal kinase domain of RSK, which is in agreement with previous genetic studies of RSK in the circadian clock but argues against the prevailing view that only the N-terminal kinase domain of RSK proteins carries the effector function. Our data provide a mechanistic explanation how RSK influences the molecular clock and imply SGG S9 phosphorylation by RSK and other kinases as a convergence point for diverse cellular and external stimuli.
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Affiliation(s)
- Katherina Beck
- Institute of Medical Radiation and Cell Research, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Anna Hovhanyan
- Institute of Medical Radiation and Cell Research, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Pamela Menegazzi
- Institute of Neurobiology and Genetics, Biozentrum, University of Würzburg, Würzburg, Germany
| | | | - Thomas Raabe
- Institute of Medical Radiation and Cell Research, Biozentrum, University of Würzburg, Würzburg, Germany
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35
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Circadian Rhythms and Sleep in Drosophila melanogaster. Genetics 2017; 205:1373-1397. [PMID: 28360128 DOI: 10.1534/genetics.115.185157] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
The advantages of the model organism Drosophila melanogaster, including low genetic redundancy, functional simplicity, and the ability to conduct large-scale genetic screens, have been essential for understanding the molecular nature of circadian (∼24 hr) rhythms, and continue to be valuable in discovering novel regulators of circadian rhythms and sleep. In this review, we discuss the current understanding of these interrelated biological processes in Drosophila and the wider implications of this research. Clock genes period and timeless were first discovered in large-scale Drosophila genetic screens developed in the 1970s. Feedback of period and timeless on their own transcription forms the core of the molecular clock, and accurately timed expression, localization, post-transcriptional modification, and function of these genes is thought to be critical for maintaining the circadian cycle. Regulators, including several phosphatases and kinases, act on different steps of this feedback loop to ensure strong and accurately timed rhythms. Approximately 150 neurons in the fly brain that contain the core components of the molecular clock act together to translate this intracellular cycling into rhythmic behavior. We discuss how different groups of clock neurons serve different functions in allowing clocks to entrain to environmental cues, driving behavioral outputs at different times of day, and allowing flexible behavioral responses in different environmental conditions. The neuropeptide PDF provides an important signal thought to synchronize clock neurons, although the details of how PDF accomplishes this function are still being explored. Secreted signals from clock neurons also influence rhythms in other tissues. SLEEP is, in part, regulated by the circadian clock, which ensures appropriate timing of sleep, but the amount and quality of sleep are also determined by other mechanisms that ensure a homeostatic balance between sleep and wake. Flies have been useful for identifying a large set of genes, molecules, and neuroanatomic loci important for regulating sleep amount. Conserved aspects of sleep regulation in flies and mammals include wake-promoting roles for catecholamine neurotransmitters and involvement of hypothalamus-like regions, although other neuroanatomic regions implicated in sleep in flies have less clear parallels. Sleep is also subject to regulation by factors such as food availability, stress, and social environment. We are beginning to understand how the identified molecules and neurons interact with each other, and with the environment, to regulate sleep. Drosophila researchers can also take advantage of increasing mechanistic understanding of other behaviors, such as learning and memory, courtship, and aggression, to understand how sleep loss impacts these behaviors. Flies thus remain a valuable tool for both discovery of novel molecules and deep mechanistic understanding of sleep and circadian rhythms.
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36
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Ni JD, Baik LS, Holmes TC, Montell C. A rhodopsin in the brain functions in circadian photoentrainment in Drosophila. Nature 2017; 545:340-344. [PMID: 28489826 PMCID: PMC5476302 DOI: 10.1038/nature22325] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 03/30/2017] [Indexed: 11/09/2022]
Abstract
Animals partition their daily activity rhythms through their internal circadian clocks, which are synchronized by oscillating day-night cycles of light. The fruit fly, Drosophila melanogaster, senses day/night cycles in part through rhodopsin-dependent light reception in the compound eye, and photoreceptor cells in the Hofbauer-Buchner (H-B) eyelet1. However, a more significant light entrainment pathway is mediated in central pacemaker neurons in the brain. The Drosophila circadian clock is extremely light sensitive. However, the only known light sensor in pacemaker neurons, the flavoprotein, cryptochrome (Cry)2,3, responds only to high levels of light in vitro4. These observations indicate the existence of an additional light-sensing pathway in fly pacemaker neurons5. Here, we identified an uncharacterized rhodopsin, Rh7, which functions in circadian light entrainment through circadian pacemaker neurons in the brain. The pacemaker neurons respond to violet light, which was dependent on Rh7. While loss of either cry or rh7 caused minor affects on photoentrainment, the defects in the double mutant were profound. The circadian photoresponse to constant light was impaired in the rh7 mutant, especially under dim light. The demonstration that Rh7 functions in circadian pacemaker neurons represents the first role for an opsin in the central brain.
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Affiliation(s)
- Jinfei D Ni
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106, USA.,Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Lisa S Baik
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, USA
| | - Todd C Holmes
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, California 92093, USA
| | - Craig Montell
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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37
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Chi L, Zou Y, Qin L, Ma W, Hao Y, Tang Y, Luo R, Wu Z. TIMELESS contributes to the progression of breast cancer through activation of MYC. Breast Cancer Res 2017; 19:53. [PMID: 28464854 PMCID: PMC5414141 DOI: 10.1186/s13058-017-0838-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/18/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Breast cancer is the most common malignancy and the leading cause of cancer death among women. TIMELESS (TIM), a circadian rhythm regulator, has been recently implicated in the progression of human cancer. However, the role of TIM in the progression of breast cancer has not been well-characterized. METHODS Immunohistochemistry (IHC) staining was used to examine TIM levels in breast cancer specimens. Mammosphere formation analysis and side population analysis were used to examine the effect of TIM on the self-renewal of breast cancer stem cells. A wound healing assay and a Transwell assay were used to determine the role of TIM in breast cancer cell migration and invasion. A soft agar growth assay in vitro and tumorigenicity in vivo were used to determine the role of TIM in tumorigenicity. RESULTS TIM levels in both breast cancer cell lines and tissues were significantly upregulated. Patients with high TIM had poorer prognosis than patients with low TIM. Overexpression of TIM dramatically enhanced, while knockdown of TIM suppressed the self-renewal of cancer stem cells (CSCs), cell invasion and migration abilities of breast cancer cells in vitro. Moreover, overexpression of TIM significantly augmented, while knockdown of TIM reduced the tumorigenicity of breast cancer cells in vivo. Mechanism studies revealed that TIM upregulated the expression and the trans-activity of the well-known oncogene MYC. Inhibition of MYC significantly blocked the effects of TIM on CSC population, cell invasion and anchor-independent cell growth. CONCLUSION TIM plays an important role in promoting breast cancer progression and may represent a novel therapeutic target for breast cancer.
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Affiliation(s)
- Limin Chi
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Yujiao Zou
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Ling Qin
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Weifeng Ma
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yanyan Hao
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Yao Tang
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Rongcheng Luo
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China.
| | - Ziqing Wu
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China. .,Key Laboratory of Molecular Tumor Pathology of Guangdong Province, Southern Medical University, Guangzhou, 510515, China. .,Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China.
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38
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Mendoza-Viveros L, Bouchard-Cannon P, Hegazi S, Cheng AH, Pastore S, Cheng HYM. Molecular modulators of the circadian clock: lessons from flies and mice. Cell Mol Life Sci 2017; 74:1035-1059. [PMID: 27689221 PMCID: PMC11107503 DOI: 10.1007/s00018-016-2378-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/03/2016] [Accepted: 09/22/2016] [Indexed: 12/16/2022]
Abstract
Circadian timekeeping is a ubiquitous mechanism that enables organisms to maintain temporal coordination between internal biological processes and time of the local environment. The molecular basis of circadian rhythms lies in a set of transcription-translation feedback loops (TTFLs) that drives the rhythmic transcription of core clock genes, whose level and phase of expression serve as the marker of circadian time. However, it has become increasingly evident that additional regulatory mechanisms impinge upon the TTFLs to govern the properties and behavior of the circadian clock. Such mechanisms include changes in chromatin architecture, interactions with other transcription factor networks, post-transcriptional control by RNA modifications, alternative splicing and microRNAs, and post-translational regulation of subcellular trafficking and protein degradation. In this review, we will summarize the current knowledge of circadian clock regulation-from transcriptional to post-translational-drawing from literature pertaining to the Drosophila and murine circadian systems.
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Affiliation(s)
- Lucia Mendoza-Viveros
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Pascale Bouchard-Cannon
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Sara Hegazi
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Stephen Pastore
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada.
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada.
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Kwok RS, Lam VH, Chiu JC. Understanding the role of chromatin remodeling in the regulation of circadian transcription in Drosophila. Fly (Austin) 2016; 9:145-54. [PMID: 26926115 PMCID: PMC4862430 DOI: 10.1080/19336934.2016.1143993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circadian clocks enable organisms to anticipate daily changes in the environment and coordinate temporal rhythms in physiology and behavior with the 24-h day-night cycle. The robust cycling of circadian gene expression is critical for proper timekeeping, and is regulated by transcription factor binding, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Recently, it has become clear that dynamic alterations in chromatin landscape at the level of histone posttranslational modification and nucleosome density facilitate rhythms in transcription factor recruitment and RNAPII activity, and are essential for progression through activating and repressive phases of circadian transcription. Here, we discuss the characterization of the BRAHMA (BRM) chromatin-remodeling protein in Drosophila in the context of circadian clock regulation. By dissecting its catalytic vs. non-catalytic activities, we propose a model in which the non-catalytic activity of BRM functions to recruit repressive factors to limit the transcriptional output of CLOCK (CLK) during the active phase of circadian transcription, while the primary function of the ATP-dependent catalytic activity is to tune and prevent over-recruitment of negative regulators by increasing nucleosome density. Finally, we divulge ongoing efforts and investigative directions toward a deeper mechanistic understanding of transcriptional regulation of circadian gene expression at the chromatin level.
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Affiliation(s)
- Rosanna S Kwok
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
| | - Vu H Lam
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
| | - Joanna C Chiu
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
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40
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Top D, Harms E, Syed S, Adams EL, Saez L. GSK-3 and CK2 Kinases Converge on Timeless to Regulate the Master Clock. Cell Rep 2016; 16:357-367. [PMID: 27346344 PMCID: PMC4945451 DOI: 10.1016/j.celrep.2016.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/27/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022] Open
Abstract
The molecular clock relies on a delayed negative feedback loop of transcriptional regulation to generate oscillating gene expression. Although the principal components of the clock are present in all circadian neurons, different neuronal clusters have varying effects on rhythmic behavior, suggesting that the clocks they house are differently regulated. Combining biochemical and genetic techniques in Drosophila, we identify a phosphorylation program native to the master pacemaker neurons that regulates the timing of nuclear accumulation of the Period/Timeless repressor complex. GSK-3/SGG binds and phosphorylates Period-bound Timeless, triggering a CK2-mediated phosphorylation cascade. Mutations that block the hierarchical phosphorylation of Timeless in vitro also delay nuclear accumulation in both tissue culture and in vivo and predictably change rhythmic behavior. This two-kinase phosphorylation cascade is anatomically restricted to the eight master pacemaker neurons, distinguishing the regulatory mechanism of the molecular clock within these neurons from the other clocks that cooperate to govern behavioral rhythmicity.
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Affiliation(s)
- Deniz Top
- Laboratory of Genetics, The Rockefeller University, 1230 York Avenue, Box 288, New York, NY 10065, USA.
| | - Emily Harms
- Laboratory of Genetics, The Rockefeller University, 1230 York Avenue, Box 288, New York, NY 10065, USA
| | - Sheyum Syed
- Department of Physics, The University of Miami, 1320 Campo Sano Avenue, Coral Gables, FL 33146, USA
| | - Eliza L Adams
- Laboratory of Genetics, The Rockefeller University, 1230 York Avenue, Box 288, New York, NY 10065, USA
| | - Lino Saez
- Laboratory of Genetics, The Rockefeller University, 1230 York Avenue, Box 288, New York, NY 10065, USA
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41
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Circadian rhythms in neuronal activity propagate through output circuits. Nat Neurosci 2016; 19:587-95. [PMID: 26928065 PMCID: PMC5066395 DOI: 10.1038/nn.4263] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/04/2016] [Indexed: 12/14/2022]
Abstract
24hr rhythms in behavior are organized by a network of circadian pacemaker neurons. Rhythmic activity in this network is generated by intrinsic rhythms in clock neuron physiology and communication between clock neurons. However, it is poorly understood how the activity of a small number of pacemaker neurons is translated into rhythmic behavior of the whole animal. To understand this, we screened for signals that could identify circadian output circuits in Drosophila. We found that Leucokinin neuropeptide (LK) and its receptor (LK-R) are required for normal behavioral rhythms. This LK/LK-R circuit connects pacemaker neurons to brain areas that regulate locomotor activity and sleep. Our experiments revealed that pacemaker neurons impose rhythmic activity and excitability on LK and LK-R expressing neurons. We also found pacemaker neuron-dependent activity rhythms in DH44-expressing neurons, a second circadian output pathway. We conclude that rhythmic clock neuron activity propagates to multiple downstream circuits to orchestrate behavioral rhythms.
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42
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A Timeless Link Between Circadian Patterns and Disease. Trends Mol Med 2016; 22:68-81. [DOI: 10.1016/j.molmed.2015.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
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43
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Identification of Light-Sensitive Phosphorylation Sites on PERIOD That Regulate the Pace of Circadian Rhythms in Drosophila. Mol Cell Biol 2015; 36:855-70. [PMID: 26711257 DOI: 10.1128/mcb.00682-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/02/2015] [Indexed: 11/20/2022] Open
Abstract
The main components regulating the pace of circadian (≅24 h) clocks in animals are PERIOD (PER) proteins, transcriptional regulators that undergo daily changes in levels and nuclear accumulation by means of complex multisite phosphorylation programs. In the present study, we investigated the function of two phosphorylation sites, at Ser826 and Ser828, located in a putative nuclear localization signal (NLS) on the Drosophila melanogaster PER protein. These sites are phosphorylated by DOUBLETIME (DBT; Drosophila homolog of CK1δ/ε), the key circadian kinase regulating the daily changes in PER stability and phosphorylation. Mutant flies in which phosphorylation at Ser826/Ser828 is blocked manifest behavioral rhythms with periods slightly longer than 1 h and with altered temperature compensation properties. Intriguingly, although phosphorylation at these sites does not influence PER stability, timing of nuclear entry, or transcriptional autoinhibition, the phospho-occupancy at Ser826/Ser828 is rapidly stimulated by light and blocked by TIMELESS (TIM), the major photosensitive clock component in Drosophila and a crucial binding partner of PER. Our findings identify the first phosphorylation sites on core clock proteins that are acutely regulated by photic cues and suggest that some phosphosites on PER proteins can modulate the pace of downstream behavioral rhythms without altering central aspects of the clock mechanism.
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44
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Temperature compensation and temperature sensation in the circadian clock. Proc Natl Acad Sci U S A 2015; 112:E6284-92. [PMID: 26578788 DOI: 10.1073/pnas.1511215112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All known circadian clocks have an endogenous period that is remarkably insensitive to temperature, a property known as temperature compensation, while at the same time being readily entrained by a diurnal temperature oscillation. Although temperature compensation and entrainment are defining features of circadian clocks, their mechanisms remain poorly understood. Most models presume that multiple steps in the circadian cycle are temperature-dependent, thus facilitating temperature entrainment, but then insist that the effect of changes around the cycle sums to zero to enforce temperature compensation. An alternative theory proposes that the circadian oscillator evolved from an adaptive temperature sensor: a gene circuit that responds only to temperature changes. This theory implies that temperature changes should linearly rescale the amplitudes of clock component oscillations but leave phase relationships and shapes unchanged. We show using timeless luciferase reporter measurements and Western blots against TIMELESS protein that this prediction is satisfied by the Drosophila circadian clock. We also review evidence for pathways that couple temperature to the circadian clock, and show previously unidentified evidence for coupling between the Drosophila clock and the heat-shock pathway.
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45
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Lever MB, Karpova A, Kreutz MR. An Importin Code in neuronal transport from synapse-to-nucleus? Front Mol Neurosci 2015; 8:33. [PMID: 26257602 PMCID: PMC4508522 DOI: 10.3389/fnmol.2015.00033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/06/2015] [Indexed: 12/24/2022] Open
Affiliation(s)
- Michael B Lever
- RG Neuroplasticity, Leibniz Institute for Neurobiology Magdeburg, Germany
| | - Anna Karpova
- RG Neuroplasticity, Leibniz Institute for Neurobiology Magdeburg, Germany
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology Magdeburg, Germany
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Venkatesan A, Fan JY, Nauman C, Price JL. A Doubletime Nuclear Localization Signal Mediates an Interaction with Bride of Doubletime to Promote Circadian Function. J Biol Rhythms 2015; 30:302-17. [PMID: 26082158 DOI: 10.1177/0748730415588189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Doubletime (DBT) has an essential circadian role in Drosophila melanogaster because it phosphorylates Period (PER). To determine if DBT antagonism can produce distinct effects in the cytosol and nucleus, forms of a dominant negative DBT(K/R) with these 2 alternative localizations were produced. DBT has a putative nuclear localization signal (NLS), and mutation of this signal confers cytosolic localization of DBT in the lateral neurons of Drosophila clock cells in the brain. By contrast, addition of a strong NLS domain (e.g., SV40 NLS) to DBT's C terminus leads to more nuclear localization. Expression of DBT(K/R) with the mutated NLS (DBT(K/R) NLS(-)) using a timGAL4 driver does not alter the circadian period of locomotor activity, and the daily oscillations of PER detected by immunoblot and immunofluorescence persist, like those of wild-type flies. By contrast, expression of DBT(K/R) with the strong NLS (DBT(K/R) stNLS) using the timGAL4 driver lengthens period more strongly than DBT(K/R), with damped oscillations of PER phosphorylation and localization. Both DBT(K/R) and DBT(WT) without the NLS fail to interact with Bride of Doubletime (BDBT) protein, which is related to FK506-binding proteins and shown to interact with DBT to enhance its circadian function. This result suggests that the DBT(K/R) NLS(-) has lost its dominant negative property because it does not form normal clock protein complexes. DBT(WT) proteins with the same changes (NLS(-) and stNLS) also produce equivalent changes in localization that do not produce opposite period phenotypes. Additionally, a DBT(K/R) protein with both the stNLS and NLS(-) mutation does not affect circadian period, although it is nuclear, demonstrating that the lack of a dominant negative for the DBT(K/R) NLS(-) is not due to failure to localize to nuclei. Finally, bdbt RNAi increases the cytosolic localization of DBT(K/R) but not of DBT(WT), suggesting a role for BDBT in DBT kinase-dependent nuclear localization of DBT.
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Affiliation(s)
- Anandakrishnan Venkatesan
- School of Biological Sciences, Division of Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, Missouri Department of Physiology, The University of Texas Health Science Center at San Antonio STRF-Greehey North Campus, San Antonio, Texas
| | - Jin-Yuan Fan
- School of Biological Sciences, Division of Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, Missouri
| | - Christopher Nauman
- School of Biological Sciences, Division of Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, Missouri
| | - Jeffrey L Price
- School of Biological Sciences, Division of Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, Missouri School of Medicine, Department of Neurology and Cognitive Neuroscience, University of Missouri-Kansas City, Kansas City, Missouri
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Depping R, Jelkmann W, Kosyna FK. Nuclear-cytoplasmatic shuttling of proteins in control of cellular oxygen sensing. J Mol Med (Berl) 2015; 93:599-608. [PMID: 25809665 DOI: 10.1007/s00109-015-1276-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 03/04/2015] [Accepted: 03/11/2015] [Indexed: 12/11/2022]
Abstract
In order to pass through the nuclear pore complex, proteins larger than ∼40 kDa require specific nuclear transport receptors. Defects in nuclear-cytoplasmatic transport affect fundamental processes such as development, inflammation and oxygen sensing. The transcriptional response to O2 deficiency is controlled by hypoxia-inducible factors (HIFs). These are heterodimeric transcription factors of each ∼100-120 kDa proteins, consisting of one out of three different O2-labile α subunits (primarily HIF-1α) and a more constitutive 1β subunit. In the presence of O2, the α subunits are hydroxylated by specific prolyl-4-hydroxylase domain proteins (PHD1, PHD2, and PHD3) and an asparaginyl hydroxylase (factor inhibiting HIF-1, FIH-1). The prolyl hydroxylation causes recognition by von Hippel-Lindau tumor suppressor protein (pVHL), ubiquitination, and proteasomal degradation. The activity of the oxygen sensing machinery depends on dynamic intracellular trafficking. Nuclear import of HIF-1α and HIF-1β is mainly mediated by importins α and β (α/β). HIF-1α can shuttle between nucleus and cytoplasm, while HIF-1β is permanently inside the nucleus. pVHL is localized to both compartments. Nuclear import of PHD1 relies on a nuclear localization signal (NLS) and uses the classical import pathway involving importin α/β receptors. PHD2 shows an atypical NLS, and its nuclear import does not occur via the classical pathway. PHD2-mediated hydroxylation of HIF-1α occurs predominantly in the cell nucleus. Nuclear export of PHD2 involves a nuclear export signal (NES) in the N-terminus and depends on the export receptor chromosome region maintenance 1 (CRM1). Nuclear import of PHD3 is mediated by importin α/β receptors and depends on a non-classical NLS. Specific modification of the nuclear translocation of the three PHD isoforms could provide a promising strategy for the development of new therapeutic substances to tackle major diseases.
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Affiliation(s)
- Reinhard Depping
- Institute of Physiology, Centre for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany,
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