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Laothamatas I, Rasmussen ES, Green CB, Takahashi JS. Metabolic and chemical architecture of the mammalian circadian clock. Cell Chem Biol 2023; 30:1033-1052. [PMID: 37708890 PMCID: PMC10631358 DOI: 10.1016/j.chembiol.2023.08.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Circadian rhythms are endogenous periodic biological processes that occur on a daily timescale. These rhythms are generated by a transcriptional/translational feedback loop that consists of the CLOCK-BMAL1 heterodimeric transcriptional activator complex and the PER1/2-CRY1/2-CK1δ/ε repressive complex. The output pathways of this molecular feedback loop generate circadian rhythmicity in various biological processes. Among these, metabolism is a primary regulatory target of the circadian clock which can also feedback to modulate clock function. This intertwined relationship between circadian rhythms and metabolism makes circadian clock components promising therapeutic targets. Despite this, pharmacological therapeutics that target the circadian clock are relatively rare. In this review, we hope to stimulate interest in chemical chronobiology by providing a comprehensive background on the molecular mechanism of mammalian circadian rhythms and their connection to metabolism, highlighting important studies in the chemical approach to circadian research, and offering our perspectives on future developments in the field.
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Affiliation(s)
- Isara Laothamatas
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Emil Sjulstok Rasmussen
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Kulshrestha S, Devkar R. Circadian control of Nocturnin and its regulatory role in health and disease. Chronobiol Int 2023; 40:970-981. [PMID: 37400970 DOI: 10.1080/07420528.2023.2231081] [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: 05/02/2023] [Revised: 06/01/2023] [Accepted: 06/24/2023] [Indexed: 07/05/2023]
Abstract
Circadian rhythms are generated by intrinsic 24-h oscillations that anticipate the extrinsic changes associated with solar day. A conserved transcriptional-translational feedback loop generates these molecular oscillations of clock genes at the organismal and the cellular levels. One of the recently discovered outputs of circadian clock is Nocturnin (Noct) or Ccrn4l. In mice, Noct mRNA is broadly expressed in cells throughout the body, with a particularly high-amplitude rhythm in liver. NOCT belongs to the EEP family of proteins with the closest similarity to the CCR4 family of deadenylases. Multiple studies have investigated the role of Nocturnin in development, adipogenesis, lipid metabolism, inflammation, osteogenesis, and obesity. Further, mice lacking Noct (Noct KO or Noct-/-) are protected from high-fat diet-induced obesity and hepatic steatosis. Recent studies had provided new insights by investigating various aspects of Nocturnin, ranging from its sub-cellular localization to identification of its target transcripts. However, a profound understanding of its molecular function remains elusive. This review article seeks to integrate the available literature into our current understanding of the functions of Nocturnin, their regulatory roles in key tissues and to throw light on the existing scientific lacunae.
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Affiliation(s)
- Shruti Kulshrestha
- Chronobiology and Molecular Endocrinology Lab, Department of Zoology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Ranjitsinh Devkar
- Chronobiology and Molecular Endocrinology Lab, Department of Zoology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
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O'Siorain JR, Curtis AM. Circadian Control of Redox Reactions in the Macrophage Inflammatory Response. Antioxid Redox Signal 2022; 37:664-678. [PMID: 35166129 DOI: 10.1089/ars.2022.0014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Significance: Macrophages are immune sentinels located throughout the body that function in both amplification and resolution of the inflammatory response. The circadian clock has emerged as a central regulator of macrophage inflammation. Reduction-oxidation (redox) reactions are central to both the circadian clock and macrophage function. Recent Advances: Circadian regulation of metabolism controls the macrophage inflammatory response, whereby disruption of the clock causes dysfunctional inflammation. Altering metabolism and reactive oxygen/nitrogen species (RONS) production rescues the inflammatory phenotype of clock-disrupted macrophages. Critical Issues: The circadian clock possesses many layers of regulation. Understanding how redox reactions coordinate clock function is critical to uncover the full extent of circadian regulation of macrophage inflammation. We provide insights into how circadian regulation of redox affects macrophage pattern recognition receptor signaling, immunometabolism, phagocytosis, and inflammasome activation. Future Directions: Many diseases associated with aberrant macrophage-derived inflammation exhibit time-of-day rhythms in disease symptoms and severity and are sensitive to circadian disruption. Macrophage function is highly dependent on redox reactions that signal through RONS. Future studies are needed to evaluate the extent of circadian control of macrophage inflammation, specifically in the context of redox signaling. Antioxid. Redox Signal. 37, 664-678.
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Affiliation(s)
- James R O'Siorain
- Curtis Clock Laboratory, School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland.,Tissue Engineering Research Group (TERG), RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Annie M Curtis
- Curtis Clock Laboratory, School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland.,Tissue Engineering Research Group (TERG), RCSI University of Medicine and Health Sciences, Dublin, Ireland
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Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures. Mol Genet Genomics 2022; 297:1627-1642. [PMID: 36006456 PMCID: PMC9596584 DOI: 10.1007/s00438-022-01947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/12/2022] [Indexed: 11/01/2022]
Abstract
The catfish Ancistrus triradiatus belongs to the species-rich family Loricariidae. Loricariids display remarkable traits such as herbivory, a benthic lifestyle, the absence of scales but the presence of dermal bony plates. They are exported as ornamental fish worldwide, with escaped fishes becoming a threat locally. Although genetic and phylogenetic studies are continuously increasing and developmental genetic investigations are underway, no genome assembly has been formally proposed for Loricariidae yet. We report a high-quality genome assembly of Ancistrus triradiatus using long and short reads, and a newly assembled transcriptome. The genome assembly is composed of 9530 scaffolds, including 85.6% of ray-finned fish BUSCOs, and 26,885 predicted protein-coding genes. The genomic GC content is higher than in other catfishes, reflecting the higher metabolism associated with herbivory. The examination of the SCPP gene family indicates that the genes presumably triggering scale loss when absent, are present in the scaleless A. triradiatus, questioning their explanatory role. The analysis of the opsin gene repertoire revealed that gene losses associated to the nocturnal lifestyle of catfishes were not entirely found in A. triradiatus, as the UV-sensitive opsin 5 is present. Finally, most gene family expansions were related to immunity except the gamma crystallin gene family which controls pupil shape and sub-aquatic vision. Thus, the genome of A. triradiatus reveals that fish herbivory may be related to the photic zone habitat, conditions metabolism, photoreception and visual functions. This genome is the first for the catfish suborder Loricarioidei and will serve as backbone for future genetic, developmental and conservation studies.
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Pouille CL, Ouaza S, Roels E, Behra J, Tourret M, Molinié R, Fontaine JX, Mathiron D, Gagneul D, Taminiau B, Daube G, Ravallec R, Rambaud C, Hilbert JL, Cudennec B, Lucau-Danila A. Chicory: Understanding the Effects and Effectors of This Functional Food. Nutrients 2022; 14:957. [PMID: 35267932 PMCID: PMC8912540 DOI: 10.3390/nu14050957] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
Industrial chicory has been the subject of numerous studies, most of which provide clinical observations on its health effects. Whether it is the roasted root, the flour obtained from the roots or the different classes of molecules that enter into the composition of this plant, understanding the molecular mechanisms of action on the human organism remains incomplete. In this study, we were interested in three molecules or classes of molecules present in chicory root: fructose, chlorogenic acids, and sesquiterpene lactones. We conducted experiments on the murine model and performed a nutrigenomic analysis, a metabolic hormone assay and a gut microbiota analysis, associated with in vitro observations for different responses. We have highlighted a large number of effects of all these classes of molecules that suggest a pro-apoptotic activity, an anti-inflammatory, antimicrobial, antioxidant, hypolipidemic and hypoglycemic effect and also an important role in appetite regulation. A significant prebiotic activity was also identified. Fructose seems to be the most involved in these activities, contributing to approximately 83% of recorded responses, but the other classes of tested molecules have shown a specific role for these different effects, with an estimated contribution of 23-24%.
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Affiliation(s)
- Céline L. Pouille
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Souad Ouaza
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Elise Roels
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Josette Behra
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Melissa Tourret
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Roland Molinié
- UMR Transfontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—BIOlogie des Plantes et Innovation (BIOPI), 80025 Amiens, France; (R.M.); (J.-X.F.)
| | - Jean-Xavier Fontaine
- UMR Transfontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—BIOlogie des Plantes et Innovation (BIOPI), 80025 Amiens, France; (R.M.); (J.-X.F.)
| | - David Mathiron
- Plateforme Analytique UFR des Sciences, UPJV, Bâtiment Serres-Transfert Rue Dallery-Passage du Sourire d’Avril, 80039 Amiens, France;
| | - David Gagneul
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Bernard Taminiau
- Department of Food Sciences–Microbiology, FARAH, University of Liege, 4000 Liege, Belgium; (B.T.); (G.D.)
| | - Georges Daube
- Department of Food Sciences–Microbiology, FARAH, University of Liege, 4000 Liege, Belgium; (B.T.); (G.D.)
| | - Rozenn Ravallec
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Caroline Rambaud
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Jean-Louis Hilbert
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Benoit Cudennec
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Anca Lucau-Danila
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
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Suchocki T, Czech B, Dunislawska A, Slawinska A, Derebecka N, Wesoly J, Siwek M, Szyda J. SNP prioritization in targeted sequencing data associated with humoral immune responses in chicken. Poult Sci 2021; 100:101433. [PMID: 34551372 PMCID: PMC8458985 DOI: 10.1016/j.psj.2021.101433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/13/2021] [Accepted: 08/15/2021] [Indexed: 11/30/2022] Open
Abstract
Our study aimed to identify single nucleotide polymorphisms (SNPs) with a significant impact on the innate immunity represented by antibody response against lipopolysaccharide (LPS) and lipoteichoid acid (LTA) and the adaptive immune response represented toward keyhole limpet hemocyanin (KLH) using the SNP prioritization method. Data set consisted of 288 F2 experimental individuals, created by crossing Green-legged Partridgelike and White Leghorn. The analyzed SNPs were located within 24 short genomic regions of GGA1, GGA2, GGA3, GGA4, GGA9, GGA10, GGA14, GGA18, and GGZ, pre-targeted based on literature references and database information. For the specific antibody response toward KLH at d 0 the most highly prioritized SNP for additive and dominance effects were located on GGA2 in the 3’UTR of MYD88. For the response at d 7, the most highly prioritized SNP pointed at the 3’UTR of MYD88, but potential causal additive variants were located within ADIPOQ and one in PROCR. The highest priority for additive and dominance effects in the antibody response toward lipoteichoic acid at d 0 was attributed to the same SNP, located on GGA2 in the 3’UTR region of MYD88. Two SNPs among the top-10 for additive effect were located in the exon of NOCT. SNPs selected for their additive effect on antibody response toward lipopolysaccharide at d 0 marked 3 genes – NOCT, MYD88, and SNX8, while SNPs selected for their dominance effect marked – NOCT, ADIPOQ, and MYD88. The top-10 variants identified in our study were located in different functional parts of the genome. In the context of causality three groups can be distinguished: variants located in exons of protein coding genes (ADIPOQ, NOCT, PROCR, SNX8), variants within exons of non-coding transcripts, and variants located in genes’ UTR regions. Variants from the first group influence protein structure and variants from both latter groups’ exhibit regulatory roles on DNA (UTR) or RNA (lncRNA).
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Affiliation(s)
- Tomasz Suchocki
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland; National Research Institute of Animal Production, Balice, Poland
| | - Bartosz Czech
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aleksandra Dunislawska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz 85-084, Poland
| | - Anna Slawinska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz 85-084, Poland
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Maria Siwek
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz 85-084, Poland.
| | - Joanna Szyda
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland; National Research Institute of Animal Production, Balice, Poland
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Marcos AT, Ramos MS, Schinko T, Strauss J, Cánovas D. Nitric oxide homeostasis is required for light-dependent regulation of conidiation in Aspergillus. Fungal Genet Biol 2020; 137:103337. [PMID: 31991229 DOI: 10.1016/j.fgb.2020.103337] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 01/24/2023]
Abstract
Nitric oxide (NO) can be biologically synthesized from nitrite or from arginine. Although NO is involved as a signal in many biological processes in bacteria, plants, and mammals, still little is known about the role of NO in fungi. Here we show that NO levels are regulated by light as an environmental signal in Aspergillus nidulans. The flavohaemoglobin-encoding fhbB gene involved in NO oxidation to nitrate, and the arginine-regulated arginase encoded by agaA, which controls the intracellular concentration of arginine, are both up-regulated by light. The phytochrome fphA is required for the light-dependent induction of fhbB and agaA, while the white-collar gene lreA acts as a repressor when arginine is present in the media. The intracellular arginine pools increase upon induction of both developmental programs (conidiation and sexual development), and the increase is higher under conditions promoting sexual development. The presence of low concentrations of arginine does not affect the light-dependent regulation of conidiation, but high concentrations of arginine overrun the light signal. Deletion of fhbB results in the partial loss of the light regulation of conidiation on arginine and on nitrate media, while deletion of fhbA only affects the light regulation of conidiation on nitrate media. Our working model considers a cross-talk between environmental cues and intracellular signals to regulate fungal reproduction.
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Affiliation(s)
- Ana T Marcos
- Department of Genetics, Faculty of Biology, University of Seville, Spain
| | - María S Ramos
- Department of Genetics, Faculty of Biology, University of Seville, Spain
| | - Thorsten Schinko
- Department of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Science, University and Research Center - Campus Tulln, Tulln - Donau, Austria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Science, University and Research Center - Campus Tulln, Tulln - Donau, Austria
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Spain; Department of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Science, University and Research Center - Campus Tulln, Tulln - Donau, Austria.
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8
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Spatiotemporal regulation of NADP(H) phosphatase Nocturnin and its role in oxidative stress response. Proc Natl Acad Sci U S A 2019; 117:993-999. [PMID: 31879354 DOI: 10.1073/pnas.1913712117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An intimate link exists between circadian clocks and metabolism with nearly every metabolic pathway in the mammalian liver under circadian control. Circadian regulation of metabolism is largely driven by rhythmic transcriptional activation of clock-controlled genes. Among these output genes, Nocturnin (Noct) has one of the highest amplitude rhythms at the mRNA level. The Noct gene encodes a protein (NOC) that is highly conserved with the endonuclease/exonuclease/phosphatase (EEP) domain-containing CCR4 family of deadenylases, but highly purified NOC possesses little or no ribonuclease activity. Here, we show that NOC utilizes the dinucleotide NADP(H) as a substrate, removing the 2' phosphate to generate NAD(H), and is a direct regulator of oxidative stress response through its NADPH 2' phosphatase activity. Furthermore, we describe two isoforms of NOC in the mouse liver. The cytoplasmic form of NOC is constitutively expressed and associates externally with membranes of other organelles, including the endoplasmic reticulum, via N-terminal glycine myristoylation. In contrast, the mitochondrial form of NOC possesses high-amplitude circadian rhythmicity with peak expression level during the early dark phase. These findings suggest that NOC regulates local intracellular concentrations of NADP(H) in a manner that changes over the course of the day.
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Onder Y, Laothamatas I, Berto S, Sewart K, Kilaru G, Bordieanu B, Stubblefield JJ, Konopka G, Mishra P, Green CB. The Circadian Protein Nocturnin Regulates Metabolic Adaptation in Brown Adipose Tissue. iScience 2019; 19:83-92. [PMID: 31357170 PMCID: PMC6664146 DOI: 10.1016/j.isci.2019.07.016] [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: 01/09/2019] [Revised: 05/20/2019] [Accepted: 07/11/2019] [Indexed: 01/19/2023] Open
Abstract
Fine-tuning of transcriptional responses can be critical for long-term outcomes in response to an environmental challenge. The circadian protein Nocturnin belongs to a family of proteins that include exonucleases, endonucleases, and phosphatases and is most closely related to the CCR4 family of deadenylases that regulate the cellular transcriptome via control of poly(A) tail length of RNA transcripts. In this study, we investigate the role of Nocturnin in regulating the transcriptional response and downstream metabolic adaptations during cold exposure in brown adipose tissue. We find that Nocturnin exhibits dual localization within the cytosol and mitochondria, and loss of Nocturnin causes changes in expression of networks of mRNAs involved in mitochondrial function. Furthermore, Nocturnin−/− animals display significantly elevated levels of tricarboxylic acid cycle intermediates, indicating that they have distinct metabolic adaptations during a prolonged cold exposure. We conclude that cold-induced stimulation of Nocturnin levels can regulate long-term metabolic adaptations to environmental challenges. Nocturnin localizes to both the cytosol and the mitochondria Nocturnin is robustly induced in response to cold exposure in brown fat Regulation of mitochondrial metabolic genes is altered in Nocturnin−/− brown fat Nocturnin regulates long-term metabolic adaptation to cold exposure in brown fat
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Affiliation(s)
- Yasemin Onder
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Isara Laothamatas
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Katharina Sewart
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gokhul Kilaru
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bogdan Bordieanu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeremy J Stubblefield
- Department of Cell Systems & Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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10
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Estrella MA, Du J, Chen L, Rath S, Prangley E, Chitrakar A, Aoki T, Schedl P, Rabinowitz J, Korennykh A. The metabolites NADP + and NADPH are the targets of the circadian protein Nocturnin (Curled). Nat Commun 2019; 10:2367. [PMID: 31147539 PMCID: PMC6542800 DOI: 10.1038/s41467-019-10125-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
Nocturnin (NOCT) is a rhythmically expressed protein that regulates metabolism under the control of circadian clock. It has been proposed that NOCT deadenylates and regulates metabolic enzyme mRNAs. However, in contrast to other deadenylases, purified NOCT lacks the deadenylase activity. To identify the substrate of NOCT, we conducted a mass spectrometry screen and report that NOCT specifically and directly converts the dinucleotide NADP+ into NAD+ and NADPH into NADH. Further, we demonstrate that the Drosophila NOCT ortholog, Curled, has the same enzymatic activity. We obtained the 2.7 Å crystal structure of the human NOCT•NADPH complex, which revealed that NOCT recognizes the chemically unique ribose-phosphate backbone of the metabolite, placing the 2′-terminal phosphate productively for removal. We provide evidence for NOCT targeting to mitochondria and propose that NADP(H) regulation, which takes place at least in part in mitochondria, establishes the molecular link between circadian clock and metabolism. Nocturnin is a rhythmically expressed protein that regulates metabolism under the control of circadian clock proposed to function through the deadenylation of metabolic enzyme mRNAs. Here the authors show that Nocturnin and its fly homolog Curled catalyze the removal of 2′-phosphate from NADP+ and NADPH, providing a direct link to metabolic regulation.
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Affiliation(s)
- Michael A Estrella
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA
| | - Jin Du
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA
| | - Li Chen
- 285 Frick Laboratory, Department of Chemistry, Princeton, NJ, 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ, 08544, USA
| | - Sneha Rath
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA
| | - Eliza Prangley
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA
| | - Alisha Chitrakar
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA
| | - Tsutomu Aoki
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA
| | - Paul Schedl
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA
| | - Joshua Rabinowitz
- 285 Frick Laboratory, Department of Chemistry, Princeton, NJ, 08544, USA. .,Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ, 08544, USA.
| | - Alexei Korennykh
- 216 Schultz Laboratory, Department of Molecular Biology, Princeton, NJ, 08544, USA.
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11
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Stubblefield JJ, Gao P, Kilaru G, Mukadam B, Terrien J, Green CB. Temporal Control of Metabolic Amplitude by Nocturnin. Cell Rep 2019; 22:1225-1235. [PMID: 29386110 PMCID: PMC5815321 DOI: 10.1016/j.celrep.2018.01.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/20/2017] [Accepted: 01/03/2018] [Indexed: 01/08/2023] Open
Abstract
The timing of food intake and nutrient utilization is critical to health and regulated partly by the circadian clock. Increased amplitude of circadian oscillations and metabolic output has been found to improve health in diabetic and obesity mouse models. Here, we report a function for the circadian deadenylase Nocturnin as a regulator of metabolic amplitude across the day/night cycle and in response to nutrient challenge. We show that mice lacking Nocturnin (Noct−/−) display significantly increased amplitudes of mRNA expression of hepatic genes encoding key metabolic enzymes regulating lipid and cholesterol synthesis, both over the daily circadian cycle and in response to fasting and refeeding. Noct−/− mice have increased plasma triglyceride throughout the night and increased amplitude of hepatic cholesterol levels. Therefore, posttranscriptional control by Nocturnin regulates the amplitude of these critical metabolic pathways, and loss of this activity results in increased metabolic flux and reduced obesity.
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Affiliation(s)
- Jeremy J Stubblefield
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.
| | - Peng Gao
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Gokhul Kilaru
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Bilal Mukadam
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Jeremy Terrien
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.
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12
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Hughes KL, Abshire ET, Goldstrohm AC. Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries. RNA Biol 2018; 15:1255-1267. [PMID: 30257600 PMCID: PMC6284557 DOI: 10.1080/15476286.2018.1526541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional control of messenger RNA (mRNA) is an important layer of gene regulation that modulates mRNA decay, translation, and localization. Eukaryotic mRNA decay begins with the catalytic removal of the 3' poly-adenosine tail by deadenylase enzymes. Multiple deadenylases have been identified in vertebrates and are known to have distinct biological roles; among these proteins is Nocturnin, which has been linked to circadian biology, adipogenesis, osteogenesis, and obesity. Multiple studies have investigated Nocturnin's involvement in these processes; however, a full understanding of its molecular function remains elusive. Recent studies have provided new insights by identifying putative Nocturnin-regulated mRNAs in mice and by determining the structure and regulatory activities of human Nocturnin. This review seeks to integrate these new discoveries into our understanding of Nocturnin's regulatory functions and highlight the important remaining unanswered questions surrounding its regulation, biochemical activities, protein partners, and target mRNAs.
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Affiliation(s)
- Kelsey L. Hughes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth T. Abshire
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Aaron C. Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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13
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Mogi A, Yomoda R, Kimura S, Tsushima C, Takouda J, Sawauchi M, Maekawa T, Ohta H, Nishino S, Kurita M, Mano N, Osumi N, Moriya T. Entrainment of the Circadian Clock in Neural Stem Cells by Epidermal Growth Factor is Closely Associated with ERK1/2-mediated Induction of Multiple Clock-related Genes. Neuroscience 2018. [DOI: 10.1016/j.neuroscience.2018.02.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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Blanco AM, Gómez-Boronat M, Madera D, Valenciano AI, Alonso-Gómez AL, Delgado MJ. First evidence of nocturnin in fish: two isoforms in goldfish differentially regulated by feeding. Am J Physiol Regul Integr Comp Physiol 2017; 314:R304-R312. [PMID: 29070504 DOI: 10.1152/ajpregu.00241.2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nocturnin (NOC) is a unique deadenylase with robust rhythmic expression involved in the regulation of metabolic processes in mammals. Currently, the possible presence of NOC in fish is unknown. This report aimed to identify NOC in a fish model, the goldfish ( Carassius auratus), and to study the possible regulation of its expression by feeding. Two partial-length cDNAs of 293 and 223 bp, named nocturnin-a ( noc-a) and nocturnin-b ( noc-b), were identified and found to be highly conserved among vertebrates. Both mRNAs show a similar widespread distribution in central and peripheral tissues, with higher levels detected for noc-a compared with noc-b. The periprandial expression profile revealed that noc-a mRNAs rise sharply after a meal in hypothalamus, intestinal bulb, and liver, whereas almost no changes were observed for noc-b. Food deprivation was found to exert opposite effects on the expression of both NOCs (generally inhibitory for noc-a, and stimulatory for noc-b) in the three mentioned tissues. A single meal after a 48-h food deprivation period reversed (totally or partially) the fasting-induced decreases in noc-a transcripts in all studied tissues and the increases in noc-b expression in the intestinal bulb. Together, this study offers the first report of NOC in fish and shows a high dependence of its expression on feeding and nutritional status. The differential responses to feeding of the two NOCs raise the possibility that they might be underlying different physiological mechanisms (e.g., food intake, lipid mobilization, energy homeostasis) in fish.
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Affiliation(s)
- Ayelén M Blanco
- Departamento de Fisiología (Fisiología Animal II), Facultad de Biología, Universidad Complutense de Madrid , Madrid , Spain
| | - Miguel Gómez-Boronat
- Departamento de Fisiología (Fisiología Animal II), Facultad de Biología, Universidad Complutense de Madrid , Madrid , Spain
| | - Diego Madera
- Departamento de Fisiología (Fisiología Animal II), Facultad de Biología, Universidad Complutense de Madrid , Madrid , Spain
| | - Ana I Valenciano
- Departamento de Fisiología (Fisiología Animal II), Facultad de Biología, Universidad Complutense de Madrid , Madrid , Spain
| | - Angel L Alonso-Gómez
- Departamento de Fisiología (Fisiología Animal II), Facultad de Biología, Universidad Complutense de Madrid , Madrid , Spain
| | - María J Delgado
- Departamento de Fisiología (Fisiología Animal II), Facultad de Biología, Universidad Complutense de Madrid , Madrid , Spain
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15
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Kojima S, Gendreau KL, Sher-Chen EL, Gao P, Green CB. Changes in poly(A) tail length dynamics from the loss of the circadian deadenylase Nocturnin. Sci Rep 2015; 5:17059. [PMID: 26586468 PMCID: PMC4653638 DOI: 10.1038/srep17059] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 10/21/2015] [Indexed: 12/15/2022] Open
Abstract
mRNA poly(A) tails are important for mRNA stability and translation, and enzymes that regulate the poly(A) tail length significantly impact protein profiles. There are eleven putative deadenylases in mammals, and it is thought that each targets specific transcripts, although this has not been clearly demonstrated. Nocturnin (NOC) is a unique deadenylase with robustly rhythmic expression and loss of Noc in mice (Noc KO) results in resistance to diet-induced obesity. In an attempt to identify target transcripts of NOC, we performed “poly(A)denylome” analysis, a method that measures poly(A) tail length of transcripts in a global manner, and identified 213 transcripts that have extended poly(A) tails in Noc KO liver. These transcripts share unexpected characteristics: they are short in length, have long half-lives, are actively translated, and gene ontology analyses revealed that they are enriched in functions in ribosome and oxidative phosphorylation pathways. However, most of these transcripts do not exhibit rhythmicity in poly(A) tail length or steady-state mRNA level, despite Noc’s robust rhythmicity. Therefore, even though the poly(A) tail length dynamics seen between genotypes may not result from direct NOC deadenylase activity, these data suggest that NOC exerts strong effects on physiology through direct and indirect control of target mRNAs.
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Affiliation(s)
- Shihoko Kojima
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111.,Department of Biological Sciences, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA, 24061
| | - Kerry L Gendreau
- Department of Biological Sciences, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA, 24061
| | - Elaine L Sher-Chen
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111
| | - Peng Gao
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111
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16
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Yang Y, Yu T, Lian YJ, Ma R, Yang S, Cho JY. Nitric oxide synthase inhibitors: a review of patents from 2011 to the present. Expert Opin Ther Pat 2014; 25:49-68. [PMID: 25380586 DOI: 10.1517/13543776.2014.979154] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Nitric oxide synthases (NOSs) are a family of enzymes that play an essential role in synthesizing nitric oxide (NO) by oxidizing l-arginine. As previously reported, NO is a significant mediator in cellular signaling pathways. It serves as a crucial regulator in insulin secretion, vascular tone, peristalsis, angiogenesis, neural development and inflammation. Due to its important role, the inhibition of these vital enzymes provides, as tools, the opportunity to gain an insight into potential therapeutic applications targeting NOSs. AREAS COVERED This paper reviews the patent literature between 2011 and mid-2014 that specified inhibitors of NOS family members as the significant targets. Google and Baidu search engines were used to find relevant patents and clinical information using NOSs or NOS inhibitor as search terms. EXPERT OPINION Considerable recent progress has been made in the development of NOS inhibitors with pharmacodynamic and pharmacokinetic properties, and such development is likely to continue. The patented compounds attenuated mostly embodying evidence from in vitro and in vivo trials that demonstrate good potential for future clinical human trials and industrial applications. Furthermore, new techniques such as X-ray ligand crystallographic study and structure-activity relationship were popularly utilized, which give new insights for developing novel, safe, efficient and selective NOS inhibitors.
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Affiliation(s)
- Yanyan Yang
- Institute for Translational Medicine, College of Medicine, Qingdao University , Qingdao 266021 , China
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17
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Hardeland R. Melatonin, noncoding RNAs, messenger RNA stability and epigenetics--evidence, hints, gaps and perspectives. Int J Mol Sci 2014; 15:18221-52. [PMID: 25310649 PMCID: PMC4227213 DOI: 10.3390/ijms151018221] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/21/2014] [Accepted: 09/24/2014] [Indexed: 02/06/2023] Open
Abstract
Melatonin is a highly pleiotropic regulator molecule, which influences numerous functions in almost every organ and, thus, up- or down-regulates many genes, frequently in a circadian manner. Our understanding of the mechanisms controlling gene expression is actually now expanding to a previously unforeseen extent. In addition to classic actions of transcription factors, gene expression is induced, suppressed or modulated by a number of RNAs and proteins, such as miRNAs, lncRNAs, piRNAs, antisense transcripts, deadenylases, DNA methyltransferases, histone methylation complexes, histone demethylases, histone acetyltransferases and histone deacetylases. Direct or indirect evidence for involvement of melatonin in this network of players has originated in different fields, including studies on central and peripheral circadian oscillators, shift work, cancer, inflammation, oxidative stress, aging, energy expenditure/obesity, diabetes type 2, neuropsychiatric disorders, and neurogenesis. Some of the novel modulators have also been shown to participate in the control of melatonin biosynthesis and melatonin receptor expression. Future work will need to augment the body of evidence on direct epigenetic actions of melatonin and to systematically investigate its role within the network of oscillating epigenetic factors. Moreover, it will be necessary to discriminate between effects observed under conditions of well-operating and deregulated circadian clocks, and to explore the possibilities of correcting epigenetic malprogramming by melatonin.
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Affiliation(s)
- Rüdiger Hardeland
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Berliner Str. 28, Göttingen D-37073, Germany.
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18
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Ribonucleoprotein complexes that control circadian clocks. Int J Mol Sci 2013; 14:9018-36. [PMID: 23698761 PMCID: PMC3676770 DOI: 10.3390/ijms14059018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/07/2013] [Accepted: 04/15/2013] [Indexed: 12/03/2022] Open
Abstract
Circadian clocks are internal molecular time-keeping mechanisms that enable organisms to adjust their physiology and behavior to the daily surroundings. Misalignment of circadian clocks leads to both physiological and health impairment. Post-transcriptional regulation and translational regulation of circadian clocks have been extensively investigated. In addition, accumulating evidence has shed new light on the involvement of ribonucleoprotein complexes (RNPs) in the post-transcriptional regulation of circadian clocks. Numerous RNA-binding proteins (RBPs) and RNPs have been implicated in the post-transcriptional modification of circadian clock proteins in different model organisms. Herein, we summarize the advances in the current knowledge on the role of RNP complexes in circadian clock regulation.
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19
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Nocturnin in the demosponge Suberites domuncula: a potential circadian clock protein controlling glycogenin synthesis in sponges. Biochem J 2013; 448:233-42. [PMID: 22928820 DOI: 10.1042/bj20120357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sponges are filter feeders that consume a large amount of energy to allow a controlled filtration of water through their aquiferous canal systems. It has been shown that primmorphs, three-dimensional cell aggregates prepared from the demosponge Suberites domuncula and cultured in vitro, change their morphology depending on the light supply. Upon exposure to light, primmorphs show a faster and stronger increase in DNA, protein and glycogen content compared with primmorphs that remain in the dark. The sponge genome contains nocturnin, a light/dark-controlled clock gene, the protein of which shares a high sequence similarity with the related molecule of higher metazoans. The sponge nocturnin protein was found showing a poly(A)-specific 3'-exoribonuclease activity. In addition, the cDNA of the glycogenin gene was identified for subsequent expression studies. Antibodies against nocturnin were raised and used in parallel with the cDNA to determine the regional expression of nocturnin in intact sponge specimens; the highest expression of nocturnin was seen in the epithelial layer around the aquiferous canals. Quantitative PCR analyses revealed that primmorphs after transfer from light to dark show a 10-fold increased expression in the nocturnin gene. In contrast, the expression level of glycogenin decreases in the dark by 3-4-fold. Exposure of primmorphs to light causes a decrease in nocturnin transcripts and a concurrent increase in glycogenin transcripts. It was concluded that sponges are provided with the molecular circadian clock protein nocturnin that is highly expressed in the dark where it controls the stability of a key metabolic enzyme, glycogenin.
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20
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Godwin AR, Kojima S, Green CB, Wilusz J. Kiss your tail goodbye: the role of PARN, Nocturnin, and Angel deadenylases in mRNA biology. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:571-9. [PMID: 23274303 DOI: 10.1016/j.bbagrm.2012.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 12/12/2012] [Accepted: 12/16/2012] [Indexed: 01/06/2023]
Abstract
PARN, Nocturnin and Angel are three of the multiple deadenylases that have been described in eukaryotic cells. While each of these enzymes appear to target poly(A) tails for shortening and influence RNA gene expression levels and quality control, the enzymes differ in terms of enzymatic mechanisms, regulation and biological impact. The goal of this review is to provide an in depth biochemical and biological perspective of the PARN, Nocturnin and Angel deadenylases. Understanding the shared and unique roles of these enzymes in cell biology will provide important insights into numerous aspects of the post-transcriptional control of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Alan R Godwin
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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21
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Gautier V, Mouton-Barbosa E, Bouyssié D, Delcourt N, Beau M, Girard JP, Cayrol C, Burlet-Schiltz O, Monsarrat B, Gonzalez de Peredo A. Label-free quantification and shotgun analysis of complex proteomes by one-dimensional SDS-PAGE/NanoLC-MS: evaluation for the large scale analysis of inflammatory human endothelial cells. Mol Cell Proteomics 2012; 11:527-39. [PMID: 22518033 PMCID: PMC3412980 DOI: 10.1074/mcp.m111.015230] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 04/10/2012] [Indexed: 12/21/2022] Open
Abstract
To perform differential studies of complex protein mixtures, strategies for reproducible and accurate quantification are needed. Here, we evaluated a quantitative proteomic workflow based on nanoLC-MS/MS analysis on an LTQ-Orbitrap-VELOS mass spectrometer and label-free quantification using the MFPaQ software. In such label-free quantitative studies, a compromise has to be found between two requirements: repeatability of sample processing and MS measurements, allowing an accurate quantification, and high proteomic coverage of the sample, allowing quantification of minor species. The latter is generally achieved through sample fractionation, which may induce experimental bias during the label-free comparison of samples processed, and analyzed independently. In this work, we wanted to evaluate the performances of MS intensity-based label-free quantification when a complex protein sample is fractionated by one-dimensional SDS-PAGE. We first tested the efficiency of the analysis without protein fractionation and could achieve quite good quantitative repeatability in single-run analysis (median coefficient of variation of 5%, 99% proteins with coefficient of variation <48%). We show that sample fractionation by one-dimensional SDS-PAGE is associated with a moderate decrease of quantitative measurement repeatability while largely improving the depth of proteomic coverage. We then applied the method for a large scale proteomic study of the human endothelial cell response to inflammatory cytokines, such as TNFα, interferon γ, and IL1β, which allowed us to finely decipher at the proteomic level the biological pathways involved in endothelial cell response to proinflammatory cytokines.
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Affiliation(s)
- Violette Gautier
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - David Bouyssié
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Nicolas Delcourt
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Mathilde Beau
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Jean-Philippe Girard
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Corinne Cayrol
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Odile Burlet-Schiltz
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Bernard Monsarrat
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Anne Gonzalez de Peredo
- From ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France, and
- §Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
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22
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Stubblefield JJ, Terrien J, Green CB. Nocturnin: at the crossroads of clocks and metabolism. Trends Endocrinol Metab 2012; 23:326-33. [PMID: 22608110 PMCID: PMC3389576 DOI: 10.1016/j.tem.2012.03.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/28/2012] [Accepted: 03/30/2012] [Indexed: 02/06/2023]
Abstract
Many aspects of metabolism exhibit daily rhythmicity under the control of endogenous circadian clocks, and disruptions in circadian timing result in dysfunctions associated with the metabolic syndrome. Nocturnin (Noc) is a robustly rhythmic gene that encodes a deadenylase thought to be involved in the removal of polyA tails from mRNAs. Mice lacking the Noc gene display resistance to diet-induced obesity and hepatic steatosis, due in part to reduced lipid trafficking in the small intestine. In addition, Noc appears to play important roles in other tissues and has been implicated in lipid metabolism, adipogenesis, glucose homeostasis, inflammation and osteogenesis. Therefore, Noc is a potential key post-transcriptional mediator in the circadian control of many metabolic processes.
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Affiliation(s)
- Jeremy J Stubblefield
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, NB4.204G, Dallas, TX 75390-9111, USA
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