1
|
de la Torre M, Pomorski A. Investigation of metal ion binding biomolecules one molecule at a time. Front Chem 2024; 12:1378447. [PMID: 38680456 PMCID: PMC11045889 DOI: 10.3389/fchem.2024.1378447] [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: 01/29/2024] [Accepted: 03/22/2024] [Indexed: 05/01/2024] Open
Abstract
Metal ions can perform multiple roles ranging from regulatory to structural and are crucial for cell function. While some metal ions like Na+ are ubiquitously present at high concentrations, other ions, especially Ca2+ and transition metals, such as Zn2+ or Cu+/2+ are regulated. The concentrations above or below the physiological range cause severe changes in the behavior of biomolecules that bind them and subsequently affect the cell wellbeing. This has led to the development of specialized protocols to study metal ion binding biomolecules in bulk conditions that mimic the cell environment. Recently, there is growing evidence of influence of post-transcriptional and post-translational modifications on the affinity of the metal ion binding sites. However, such targets are difficult to obtain in amounts required for classical biophysical experiments. Single molecule techniques have revolutionized the field of biophysics, molecular and structural biology. Their biggest advantage is the ability to observe each molecule's interaction independently, without the need for synchronization. An additional benefit is its extremely low sample consumption. This feature allows characterization of designer biomolecules or targets obtained coming from natural sources. All types of biomolecules, including proteins, DNA and RNA were characterized using single molecule methods. However, one group is underrepresented in those studies. These are the metal ion binding biomolecules. Single molecule experiments often require separate optimization, due to extremely different concentrations used during the experiments. In this review we focus on single molecule methods, such as single molecule FRET, nanopores and optical tweezers that are used to study metal ion binding biomolecules. We summarize various examples of recently characterized targets and reported experimental conditions. Finally, we discuss the potential promises and pitfalls of single molecule characterization on metal ion binding biomolecules.
Collapse
Affiliation(s)
| | - Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| |
Collapse
|
2
|
Yamakawa GR, Patel M, Lin R, O'Brien TJ, Mychasiuk R, Casillas‐Espinosa PM. Diurnal circadian clock gene expression is altered in models of genetic and acquired epilepsy. Epilepsia Open 2023; 8:1523-1531. [PMID: 37805809 PMCID: PMC10690682 DOI: 10.1002/epi4.12841] [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: 06/23/2023] [Accepted: 09/12/2023] [Indexed: 10/09/2023] Open
Abstract
OBJECTIVES Growing evidence demonstrates a relationship between epilepsy and the circadian system. However, relatively little is known about circadian function in disease states, such as epilepsy. This study aimed to characterize brain and peripheral core circadian clock gene expression in rat models of genetic and acquired epilepsy. METHODS For the Genetic Absence Epilepsy Rats from Strasbourg (GAERS) study, we used 40 GAERS and 40 non-epileptic control (NEC) rats. For the kainic acid status epilepticus (KASE) study, we used 40 KASE and 40 sham rats. Rats were housed in a 7 am:7 pm light-dark cycle. Hypothalamus, hippocampus, liver, and small intestine samples were collected every 3 h throughout the light period. We then assessed core diurnal clock gene expression of per1, cry1, clock, and bmal1. RESULTS In the GAERS rats, all tissues exhibited significant changes in clock gene expression (P < 0.05) when compared to NEC. In the KASE rats, there were fewer effects of the epileptic condition in the hypothalamus, hippocampus, or small intestine (P > 0.05) compared with shams. SIGNIFICANCE These results indicate marked diurnal disruption to core circadian clock gene expression in rats with both generalized and focal chronic epilepsy. This could contribute to epileptic symptomology and implicate the circadian system as a viable target for future treatments.
Collapse
Affiliation(s)
- Glenn R. Yamakawa
- Department of Neuroscience, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Meshwa Patel
- Department of Neuroscience, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Runxuan Lin
- Department of Neuroscience, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Terence J. O'Brien
- Department of Neuroscience, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
- Department of NeurologyThe Alfred HospitalMelbourneVictoriaAustralia
| | - Richelle Mychasiuk
- Department of Neuroscience, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Pablo M. Casillas‐Espinosa
- Department of Neuroscience, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
- Department of NeurologyThe Alfred HospitalMelbourneVictoriaAustralia
| |
Collapse
|
3
|
Watts AJ, Storey KB. Peripheral circadian gene activity is altered during hibernation in the thirteen-lined ground squirrel. Cryobiology 2022; 107:48-56. [DOI: 10.1016/j.cryobiol.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 01/08/2023]
|
4
|
Litovchenko M, Meireles-Filho ACA, Frochaux MV, Bevers RPJ, Prunotto A, Anduaga AM, Hollis B, Gardeux V, Braman VS, Russeil JMC, Kadener S, Dal Peraro M, Deplancke B. Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. SCIENCE ADVANCES 2021; 7:eabc3781. [PMID: 33514540 PMCID: PMC7846174 DOI: 10.1126/sciadv.abc3781] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/10/2020] [Indexed: 05/10/2023]
Abstract
Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transcriptomes of Drosophila melanogaster (w1118 ) and 141 Drosophila Genetic Reference Panel (DGRP) lines. This comprehensive circadian gene expression atlas contains >1700 cycling genes including previously unknown central circadian clock components and tissue-specific regulators. Furthermore, >30% of DGRP lines exhibited aberrant circadian gene expression, revealing abundant genetic variation-mediated, intertissue circadian expression desynchrony. Genetic analysis of one line with the strongest deviating circadian expression uncovered a novel cry mutation that, as shown by protein structural modeling and brain immunohistochemistry, disrupts the light-driven flavin adenine dinucleotide cofactor photoreduction, providing in vivo support for the importance of this conserved photoentrainment mechanism. Together, our study revealed pervasive tissue-specific circadian expression variation with genetic variants acting upon tissue-specific regulatory networks to generate local gene expression oscillations.
Collapse
Affiliation(s)
- Maria Litovchenko
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Antonio C A Meireles-Filho
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Michael V Frochaux
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Roel P J Bevers
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Alessio Prunotto
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | | | - Brian Hollis
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Vincent Gardeux
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Virginie S Braman
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Julie M C Russeil
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | | | - Matteo Dal Peraro
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| |
Collapse
|
5
|
Yamakawa G, Brady R, Sun M, McDonald S, Shultz S, Mychasiuk R. The interaction of the circadian and immune system: Desynchrony as a pathological outcome to traumatic brain injury. Neurobiol Sleep Circadian Rhythms 2020; 9:100058. [PMID: 33364525 PMCID: PMC7752723 DOI: 10.1016/j.nbscr.2020.100058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/11/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Traumatic brain injury (TBI) is a complex and costly worldwide phenomenon that can lead to many negative health outcomes including disrupted circadian function. There is a bidirectional relationship between the immune system and the circadian system, with mammalian coordination of physiological activities being controlled by the primary circadian pacemaker in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN receives light information from the external environment and in turn synchronizes rhythms throughout the brain and body. The SCN is capable of endogenous self-sustained oscillatory activity through an intricate clock gene negative feedback loop. Following TBI, the response of the immune system can become prolonged and pathophysiological. This detrimental response not only occurs in the brain, but also within the periphery, where a leaky blood brain barrier can permit further infiltration of immune and inflammatory factors. The prolonged and pathological immune response that follows TBI can have deleterious effects on clock gene cycling and circadian function not only in the SCN, but also in other rhythmic areas throughout the body. This could bring about a state of circadian desynchrony where different rhythmic structures are no longer working together to promote optimal physiological function. There are many parallels between the negative symptomology associated with circadian desynchrony and TBI. This review discusses the significant contributions of an immune-disrupted circadian system on the negative symptomology following TBI. The implications of TBI symptomology as a disorder of circadian desynchrony are discussed.
Collapse
Affiliation(s)
- G.R. Yamakawa
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - R.D. Brady
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Medicine, University of Melbourne, Parkville, Australia
| | - M. Sun
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - S.J. McDonald
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Australia
| | - S.R. Shultz
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Medicine, University of Melbourne, Parkville, Australia
| | - R. Mychasiuk
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| |
Collapse
|
6
|
A Symphony of Signals: Intercellular and Intracellular Signaling Mechanisms Underlying Circadian Timekeeping in Mice and Flies. Int J Mol Sci 2019; 20:ijms20092363. [PMID: 31086044 PMCID: PMC6540063 DOI: 10.3390/ijms20092363] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/10/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
The central pacemakers of circadian timekeeping systems are highly robust yet adaptable, providing the temporal coordination of rhythms in behavior and physiological processes in accordance with the demands imposed by environmental cycles. These features of the central pacemaker are achieved by a multi-oscillator network in which individual cellular oscillators are tightly coupled to the environmental day-night cycle, and to one another via intercellular coupling. In this review, we will summarize the roles of various neurotransmitters and neuropeptides in the regulation of circadian entrainment and synchrony within the mammalian and Drosophila central pacemakers. We will also describe the diverse functions of protein kinases in the relay of input signals to the core oscillator or the direct regulation of the molecular clock machinery.
Collapse
|
7
|
Morales-Santana S, Morell S, Leon J, Carazo-Gallego A, Jimenez-Lopez JC, Morell M. An Overview of the Polymorphisms of Circadian Genes Associated With Endocrine Cancer. Front Endocrinol (Lausanne) 2019; 10:104. [PMID: 30873119 PMCID: PMC6401647 DOI: 10.3389/fendo.2019.00104] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/04/2019] [Indexed: 12/17/2022] Open
Abstract
A major consequence of the world industrialized lifestyle is the increasing period of unnatural light in environments during the day and artificial lighting at night. This major change disrupts endogenous homeostasis with external circadian cues, which has been associated to higher risk of diseases affecting human health, mainly cancer among others. Circadian disruption promotes tumor development and accelerate its fast progression. The dysregulation mechanisms of circadian genes is greatly affected by the genetic variability of these genes. To date, several core circadian genes, also called circadian clock genes, have been identified, comprising the following: ARNTL, CLOCK, CRY1, CRY2, CSNK1E, NPAS2, NR1D1, NR1D2, PER1, PER2, PER3, RORA, and TIMELESS. The polymorphic variants of these circadian genes might contribute to an individual's risk to cancer. In this short review, we focused on clock circadian clock-related genes, major contributors of the susceptibility to endocrine-dependent cancers through affecting circadian clock, most likely affecting hormonal regulation. We examined polymorphisms affecting breast, prostate and ovarian carcinogenesis, in addition to pancreatic and thyroid cancer. Further study of the genetic composition in circadian clock-controlled tumors will be of great importance by establishing the foundation to discover novel genetic biomarkers for cancer prevention, prognosis and target therapies.
Collapse
Affiliation(s)
- Sonia Morales-Santana
- Proteomic Research Service, San Cecilio University Hospital, Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Granada, Spain
- *Correspondence: Sonia Morales-Santana
| | - Santiago Morell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Santiago Morell
| | - Josefa Leon
- Clinical Management Unit of Digestive Disease, San Cecilio University Hospital, Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Granada, Spain
| | - Angel Carazo-Gallego
- Genomic Research Service, San Cecilio University Hospital, Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Granada, Spain
| | - Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - María Morell
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain
| |
Collapse
|
8
|
Circadian Rhythms and Sleep in Drosophila melanogaster. Genetics 2017; 205:1373-1397. [PMID: 28360128 DOI: 10.1534/genetics.115.185157] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [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.
Collapse
|
9
|
Agrawal A, Khan MJ, Graugnard DE, Vailati-Riboni M, Rodriguez-Zas SL, Osorio JS, Loor JJ. Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows. Bioinform Biol Insights 2017; 11:1177932217704667. [PMID: 28579762 PMCID: PMC5414586 DOI: 10.1177/1177932217704667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Holstein cows were fed a high-straw, control-energy diet (CON; NEL = 1.34 Mcal/kg) or overfed a moderate-energy diet (OVE; NEL = 1.62 Mcal/kg) during the dry period. Blood for PMNL isolation and metabolite analysis was collected at −14 and +7 days relative to parturition. At an analysis of variance false discovery rate <0.05, energy intake (OVE vs CON) influenced 1806 genes. Dynamic Impact Approach bioinformatics analysis classified treatment effects on Kyoto Encyclopedia of Genes and Genomes pathways, including activated oxidative phosphorylation and biosynthesis of unsaturated fatty acids and inhibited RNA polymerase, proteasome, and toll-like receptor signaling pathway. This analysis indicates that processes critical for energy metabolism and cellular and immune function were affected with mixed results. However, overall interpretation of the transcriptome data agreed in part with literature documenting a potentially detrimental, chronic activation of PMNL in response to overfeeding. The widespread, transcriptome-level changes captured here confirm the importance of dietary energy adjustments around calving on the immune system.
Collapse
Affiliation(s)
- A Agrawal
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M J Khan
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D E Graugnard
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M Vailati-Riboni
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - S L Rodriguez-Zas
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - J S Osorio
- Department of Dairy Science, South Dakota State University, Brookings, SD, USA
| | - J J Loor
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
10
|
Jang AR, Moravcevic K, Saez L, Young MW, Sehgal A. Drosophila TIM binds importin α1, and acts as an adapter to transport PER to the nucleus. PLoS Genet 2015; 11:e1004974. [PMID: 25674790 PMCID: PMC4335507 DOI: 10.1371/journal.pgen.1004974] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/23/2014] [Indexed: 02/07/2023] Open
Abstract
Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop. In Drosophila, nuclear entry of the clock proteins, PERIOD (PER) and TIMELESS (TIM), is tightly controlled, and impairments of this process produce profound behavioral phenotypes. We report here that nuclear entry of PER-TIM in clock cells, and consequently behavioral rhythms, require a specific member of a classic nuclear import pathway, Importin α1 (IMPα1). In addition to IMPα1, rhythmic behavior and nuclear expression of PER-TIM require a specific nuclear pore protein, Nup153, and Ran-GTPase. IMPα1 can also drive rapid and efficient nuclear expression of TIM and PER in cultured cells, although the effect on PER is mediated by TIM. Mapping of interaction domains between IMPα1 and TIM/PER suggests that TIM is the primary cargo for the importin machinery. This is supported by attenuated interaction of IMPα1 with TIM carrying a mutation previously shown to prevent nuclear entry of TIM and PER. TIM is detected at the nuclear envelope, and computational modeling suggests that it contains HEAT-ARM repeats typically found in karyopherins, consistent with its role as a co-transporter for PER. These findings suggest that although PER is the major timekeeper of the clock, TIM is the primary target of nuclear import mechanisms. Thus, the circadian clock uses specific components of the importin pathway with a novel twist in that TIM serves a karyopherin-like role for PER. In Drosophila, circadian rhythms are driven by a negative feedback loop that includes the key regulators, period (per) and timeless (tim). To generate this feedback loop, PER and TIM proteins first accumulate in the cytoplasm and then translocate to the nucleus where PER represses transcription. Thus, the nuclear import of PER-TIM proteins is a critical step to separate the phases of activation and repression of mRNA synthesis. In this study, we discovered that a member of the nuclear import machinery, importin α1 is an essential component of this feedback loop. Flies lacking importin α1 (IMPα1) display arrhythmic behavior and cytoplasmic expression of both PER and TIM at all times. In cultured S2 cells, IMPα1 expression directly facilitates nuclear import of TIM, but the effect on PER appears to be indirect. TIM expression is detected at the nuclear envelope and it interacts with other components of the nuclear transport machinery, which we show are also required for nuclear expression of TIM-PER and for behavioral rhythms. Our results thus suggest that TIM functions to link PER to the nuclear import machinery through IMPα1. Altogether, this study provides the mechanistic basis of a crucial step in the circadian clock mechanism.
Collapse
Affiliation(s)
- A. Reum Jang
- Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katarina Moravcevic
- Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lino Saez
- Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
| | - Michael W. Young
- Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
| | - Amita Sehgal
- Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
11
|
Tataroglu O, Emery P. The molecular ticks of the Drosophila circadian clock. CURRENT OPINION IN INSECT SCIENCE 2015; 7:51-57. [PMID: 26120561 PMCID: PMC4480617 DOI: 10.1016/j.cois.2015.01.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Drosophila is a powerful model to understand the mechanisms underlying circadian rhythms. The Drosophila molecular clock is comprised of transcriptional feedback loops. The expressions of the critical transcriptional activator CLK and its repressors PER and TIM are under tight transcriptional control. However, posttranslational modification of these proteins and regulation of their stability are critical to their function and to the generation of 24-hr period rhythms. We review here recent progress made in our understanding of PER, TIM and CLK posttranslational control. We also review recent studies that are uncovering the importance of novel regulatory mechanisms that affect mRNA stability and translation of circadian pacemaker proteins and their output.
Collapse
|
12
|
Price JL, Fan JY, Keightley A, Means JC. The role of casein kinase I in the Drosophila circadian clock. Methods Enzymol 2014; 551:175-95. [PMID: 25662457 DOI: 10.1016/bs.mie.2014.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
The circadian clock mechanism in organisms as diverse as cyanobacteria and humans involves both transcriptional and posttranslational regulation of key clock components. One of the roles for the posttranslational regulation is to time the degradation of the targeted clock proteins, so that their oscillation profiles are out of phase with respect to those of the mRNAs from which they are translated. In Drosophila, the circadian transcriptional regulator PERIOD (PER) is targeted for degradation by a kinase (DOUBLETIME or DBT) orthologous to mammalian kinases (CKIɛ and CKIδ) that also target mammalian PER. Since these kinases are not regulated by second messengers, the mechanism (if any) for their regulation is not known. We are investigating the possibility that regulation of DBT is conferred by other proteins that associate with DBT and PER. In this chapter, the methods we are employing to identify and analyze these factors are discussed. These methods include expression of wild type and mutant proteins with the GAL4/UAS binary expression approach, analysis of DBT in Drosophila S2 cells, in vitro kinase assays with DBT isolated from S2 cells, and proteomic analysis of DBT-containing complexes and of DBT phosphorylation with mass spectrometry. The work has led to the discovery of a previously unrecognized circadian rhythm component (Bride of DBT, a noncanonical FK506-binding protein) and the mapping of autophosphorylation sites within the DBT C-terminal domain with potential regulatory roles.
Collapse
Affiliation(s)
- Jeffrey L Price
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA.
| | - Jin-Yuan Fan
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Andrew Keightley
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - John C Means
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
| |
Collapse
|
13
|
Collins B, Kaplan HS, Cavey M, Lelito KR, Bahle AH, Zhu Z, Macara AM, Roman G, Shafer OT, Blau J. Differentially timed extracellular signals synchronize pacemaker neuron clocks. PLoS Biol 2014; 12:e1001959. [PMID: 25268747 PMCID: PMC4181961 DOI: 10.1371/journal.pbio.1001959] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/20/2014] [Indexed: 12/22/2022] Open
Abstract
Circadian pacemaker neurons in Drosophila are regulated by two synchronizing signals that are released at opposite times of day, generating a rhythm in intracellular cyclic AMP. Synchronized neuronal activity is vital for complex processes like behavior. Circadian pacemaker neurons offer an unusual opportunity to study synchrony as their molecular clocks oscillate in phase over an extended timeframe (24 h). To identify where, when, and how synchronizing signals are perceived, we first studied the minimal clock neural circuit in Drosophila larvae, manipulating either the four master pacemaker neurons (LNvs) or two dorsal clock neurons (DN1s). Unexpectedly, we found that the PDF Receptor (PdfR) is required in both LNvs and DN1s to maintain synchronized LNv clocks. We also found that glutamate is a second synchronizing signal that is released from DN1s and perceived in LNvs via the metabotropic glutamate receptor (mGluRA). Because simultaneously reducing Pdfr and mGluRA expression in LNvs severely dampened Timeless clock protein oscillations, we conclude that the master pacemaker LNvs require extracellular signals to function normally. These two synchronizing signals are released at opposite times of day and drive cAMP oscillations in LNvs. Finally we found that PdfR and mGluRA also help synchronize Timeless oscillations in adult s-LNvs. We propose that differentially timed signals that drive cAMP oscillations and synchronize pacemaker neurons in circadian neural circuits will be conserved across species. Circadian molecular clocks are essential for daily cycles in animal behavior and we have a good understanding of how these clocks work in individual pacemaker neurons. However, the accuracy of these individual clocks is meaningless unless they are synchronized with one another. In this study we show that synchronizing the principal pacemaker LNv neurons in Drosophila larvae require two extracellular signals that are received at opposite times of day: namely, the neuropeptide PDF released from LNvs themselves at dawn and glutamate released from dorsal clock neurons at dusk. LNvs perceive both PDF and glutamate via G-protein coupled receptors that increase or decrease intracellular cAMP, respectively. The alternating phases of PDF and glutamate release generate oscillations in intracellular cyclic AMP. In addition to maintaining synchrony between LNvs, this rhythm is also required for molecular clock oscillations in individual larval LNvs. We show that disruption of PDF and glutamate signaling also reduces synchrony in adult LNvs. This impairs the oscillations of clock proteins and flies have delayed onset of sleep. Our data highlight the importance of intercellular signaling in ensuring synchrony between clock neurons within the circadian network. Our findings help extend the conservation of clock properties between Drosophila and mammals beyond clock genes to include clock circuitry.
Collapse
Affiliation(s)
- Ben Collins
- Department of Biology, New York University, New York, New York, United States of America
| | - Harris S. Kaplan
- Department of Biology, New York University, New York, New York, United States of America
| | - Matthieu Cavey
- Department of Biology, New York University, New York, New York, United States of America
| | - Katherine R. Lelito
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew H. Bahle
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Zhonghua Zhu
- Department of Biology, New York University, New York, New York, United States of America
| | - Ann Marie Macara
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gregg Roman
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Orie T. Shafer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Justin Blau
- Department of Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi Institute, Abu Dhabi, United Arab Emirates
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- * E-mail:
| |
Collapse
|