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Jia K, Jia Y, Zeng Q, Yan Z, Wang S. Regulation of Conidiation and Aflatoxin B1 Biosynthesis by a Blue Light Sensor LreA in Aspergillus flavus. J Fungi (Basel) 2024; 10:650. [PMID: 39330410 PMCID: PMC11433291 DOI: 10.3390/jof10090650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 09/04/2024] [Accepted: 09/09/2024] [Indexed: 09/28/2024] Open
Abstract
Conidia are important for the dispersal of Aspergillus flavus, which usually generates aflatoxin B1 (AFB1) and poses a threat to the safety of agricultural food. The development of conidia is usually susceptible to changes in environmental conditions, such as nutritional status and light. However, how the light signal is involved in the conidiation in A. flavus is still unknown. In this study, LreA was identified to respond to blue light and mediate the promotion of conidiation in A. flavus, which is related to the central development pathway. At the same time, blue light inhibited the biosynthesis of AFB1, which was mediated by LreA and attributed to the transcriptional regulation of aflR and aflS expression. Our findings disclosed the function and mechanism of the blue light sensor LreA in regulating conidiation and AFB1 biosynthesis, which is beneficial for the prevention and control of A. flavus and mycotoxins.
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Affiliation(s)
- Kunzhi Jia
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yipu Jia
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qianhua Zeng
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhaoqi Yan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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2
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Jankowski MS, Griffith D, Shastry DG, Pelham JF, Ginell GM, Thomas J, Karande P, Holehouse AS, Hurley JM. Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator. Nat Commun 2024; 15:3523. [PMID: 38664421 PMCID: PMC11045787 DOI: 10.1038/s41467-024-47761-z] [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: 09/07/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ in Neurospora crassa. We identified residues required for FRQ's interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant "blocks" within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.
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Affiliation(s)
- Meaghan S Jankowski
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joshua Thomas
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Pankaj Karande
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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3
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Zhang H, Zhou Z, Guo J. The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species. Int J Mol Sci 2024; 25:2574. [PMID: 38473819 DOI: 10.3390/ijms25052574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.
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Affiliation(s)
- Haoran Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zengxuan Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinhu Guo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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4
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Hu Z, Zhang N, Qin Z, Li J, Yang N, Chen Y, Kong J, Luo W, Xiong A, Zhuang J. Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants ( Camellia sinensis). Int J Mol Sci 2024; 25:657. [PMID: 38203827 PMCID: PMC10780195 DOI: 10.3390/ijms25010657] [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: 09/23/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible 'clock' in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor is involved in plant growth and development. MYB is also inextricably correlated with the circadian rhythm. In this study, the transcriptome data of the tea plant 'Baiyeyihao' were measured at a photoperiod interval of 4 h (24 h). A total of 25,306 unigenes were obtained, including 14,615 unigenes that were annotated across 20 functional categories within the GO classification. Additionally, 10,443 single-gene clusters were annotated to 11 sublevels of metabolic pathways using KEGG. Based on the results of gene annotation and differential gene transcript analysis, 22 genes encoding MYB transcription factors were identified. The G10 group in the phylogenetic tree had 13 members, of which 5 were related to the circadian rhythm, accounting for 39%. The G1, G2, G8, G9, G15, G16, G18, G19, G20, G21 and G23 groups had no members associated with the circadian rhythm. Among the 22 differentially expressed MYB transcription factors, 3 members of LHY, RVE1 and RVE8 were core circadian rhythm genes belonging to the G10, G12 and G10 groups, respectively. Real-time fluorescence quantitative PCR was used to detect and validate the expression of the gene transcripts encoding MYB transcription factors associated with the circadian rhythm.
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Affiliation(s)
- Zhihang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Nan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhiyuan Qin
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Jinwen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Jieyu Kong
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Wei Luo
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
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5
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Yu W, Pei R, Zhang Y, Tu Y, He B. Light regulation of secondary metabolism in fungi. J Biol Eng 2023; 17:57. [PMID: 37653453 PMCID: PMC10472637 DOI: 10.1186/s13036-023-00374-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
Fungi have evolved unique metabolic regulation mechanisms for adapting to the changing environments. One of the key features of fungal adaptation is the production of secondary metabolites (SMs), which are essential for survival and beneficial to the organism. Many of these SMs are produced in response to the environmental cues, such as light. In all fungal species studied, the Velvet complex transcription factor VeA is a central player of the light regulatory network. In addition to growth and development, the intensity and wavelength of light affects the formation of a broad range of secondary metabolites. Recent studies, mainly on species of the genus Aspergillus, revealed that the dimer of VeA-VelB and LaeA does not only regulate gene expression in response to light, but can also be involved in regulating production of SMs. Furthermore, the complexes have a wide regulatory effect on different types of secondary metabolites. In this review, we discussed the role of light in the regulation of fungal secondary metabolism. In addition, we reviewed the photoreceptors, transcription factors, and signaling pathways that are involved in light-dependent regulation of secondary metabolism. The effects of transcription factors on the production of secondary metabolites, as well as the potential applications of light regulation for the production of pharmaceuticals and other products were discussed. Finally, we provided an overview of the current research in this field and suggested potential areas for future research.
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Affiliation(s)
- Wenbin Yu
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Rongqiang Pei
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Yufei Zhang
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China.
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, Jiangxi, China.
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6
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Pelham JF, Mosier AE, Altshuler SC, Rhodes ML, Kirchhoff CL, Fall WB, Mann C, Baik LS, Chiu JC, Hurley JM. Conformational changes in the negative arm of the circadian clock correlate with dynamic interactomes involved in post-transcriptional regulation. Cell Rep 2023; 42:112376. [PMID: 37043358 PMCID: PMC10562519 DOI: 10.1016/j.celrep.2023.112376] [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: 12/07/2021] [Revised: 09/16/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
Biology is tuned to the Earth's diurnal cycle by the circadian clock, a transcriptional/translational negative feedback loop that regulates physiology via transcriptional activation and other post-transcriptional mechanisms. We hypothesize that circadian post-transcriptional regulation might stem from conformational shifts in the intrinsically disordered proteins that comprise the negative arm of the feedback loop to coordinate variation in negative-arm-centered macromolecular complexes. This work demonstrates temporal conformational fluidity in the negative arm that correlates with 24-h variation in physiologically diverse macromolecular complex components in eukaryotic clock proteins. Short linear motifs on the negative-arm proteins that correspond with the interactors localized to disordered regions and known temporal phosphorylation sites suggesting changes in these macromolecular complexes could be due to conformational changes imparted by the temporal phospho-state. Interactors that oscillate in the macromolecular complexes over circadian time correlate with post-transcriptionally regulated proteins, highlighting how time-of-day variation in the negative-arm protein complexes may tune cellular physiology.
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Affiliation(s)
- Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Alexander E Mosier
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Samuel C Altshuler
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Morgan L Rhodes
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | - William B Fall
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Catherine Mann
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lisa S Baik
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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7
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Chen X, Liu X, Gan X, Li S, Ma H, Zhang L, Wang P, Li Y, Huang T, Yang X, Fang L, Liang Y, Wu J, Chen T, Zhou Z, Liu X, Guo J. Differential regulation of phosphorylation, structure and stability of circadian clock protein FRQ isoforms. J Biol Chem 2023; 299:104597. [PMID: 36898580 PMCID: PMC10140173 DOI: 10.1016/j.jbc.2023.104597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 03/12/2023] Open
Abstract
Neurospora crassa is an important model for circadian clock research. The Neurospora core circadian component FRQ protein has two isoforms, large FRQ (l-FRQ) and small FRQ (s-FRQ), of which l-FRQ bears an additional N-terminal 99-amino acid fragment. However, how the FRQ isoforms operate differentially in regulating the circadian clock remains elusive. Here, we show l-FRQ and s-FRQ play different roles in regulating the circadian negative feedback loop. Compared to s-FRQ, l-FRQ is less stable at three temperatures, and undergoes hypophosphorylation and faster degradation. The phosphorylation of the C-terminal l-FRQ 794-aa fragment was markedly higher than that of s-FRQ, suggesting the l-FRQ N-terminal 99-aa region may regulate phosphorylation of the entire FRQ protein. Quantitative label-free LC/MS analysis identified several peptides that were differentially phosphorylated between l-FRQ and s-FRQ, which were distributed in FRQ in an interlaced fashion. Furthermore, we identified two novel phosphorylation sites, S765 and T781; mutations S765A and T781A showed no significant effects on conidiation rhythmicity, although T781 conferred FRQ stability. These findings demonstrate that FRQ isoforms play differential roles in the circadian negative feedback loop and undergo different regulation of phosphorylation, structure, and stability. The l-FRQ N-terminal 99-aa region plays an important role in regulating the phosphorylation, stability, conformation, and function of the FRQ protein. As the FRQ circadian clock counterparts in other species also have isoforms or paralogues, these findings will also further our understanding of the underlying regulatory mechanisms of the circadian clock in other organisms based on the high conservation of circadian clocks in eukaryotes.
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Affiliation(s)
- Xianyun Chen
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaolan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xihui Gan
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Silin Li
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huan Ma
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Peiliang Wang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yunzhen Li
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tianyu Huang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaolin Yang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ling Fang
- Sun Yat-sen University Instrumental Analysis & Research Center, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingying Liang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingjing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongyue Chen
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zengxuan Zhou
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinhu Guo
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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8
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Wang B, Stevenson EL, Dunlap JC. Functional analysis of 110 phosphorylation sites on the circadian clock protein FRQ identifies clusters determining period length and temperature compensation. G3 (BETHESDA, MD.) 2023; 13:jkac334. [PMID: 36537198 PMCID: PMC9911066 DOI: 10.1093/g3journal/jkac334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/13/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
In the negative feedback loop driving the Neurospora circadian oscillator, the negative element, FREQUENCY (FRQ), inhibits its own expression by promoting phosphorylation of its heterodimeric transcriptional activators, White Collar-1 (WC-1) and WC-2. FRQ itself also undergoes extensive time-of-day-specific phosphorylation with over 100 phosphosites previously documented. Although disrupting individual or certain clusters of phosphorylation sites has been shown to alter circadian period lengths to some extent, it is still elusive how all the phosphorylations on FRQ control its activity. In this study, we systematically investigated the role in period determination of all 110 reported FRQ phosphorylation sites, using mutagenesis and luciferase reporter assays. Surprisingly, robust FRQ phosphorylation is still detected even when 84 phosphosites were eliminated altogether; further mutating another 26 phosphoresidues completely abolished FRQ phosphorylation. To identify phosphoresidue(s) on FRQ impacting circadian period length, a series of clustered frq phosphomutants covering all the 110 phosphosites were generated and examined for period changes. When phosphosites in the N-terminal and middle regions of FRQ were eliminated, longer periods were typically seen while removal of phosphorylation in the C-terminal tail resulted in extremely short periods, among the shortest reported. Interestingly, abolishing the 11 phosphosites in the C-terminal tail of FRQ not only results in an extremely short period, but also impacts temperature compensation (TC), yielding an overcompensated circadian oscillator. In addition, the few phosphosites in the middle of FRQ are also found to be crucial for TC. When different groups of FRQ phosphomutations were combined intramolecularly, expected additive effects were generally observed except for one novel case of intramolecular epistasis, where arrhythmicity resulting from one cluster of phosphorylation site mutants was restored by eliminating phosphorylation at another group of sites.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Elizabeth-Lauren Stevenson
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
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9
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Szőke A, Sárkány O, Schermann G, Kapuy O, Diernfellner ACR, Brunner M, Gyöngyösi N, Káldi K. Adaptation to glucose starvation is associated with molecular reorganization of the circadian clock in Neurospora crassa. eLife 2023; 12:79765. [PMID: 36625037 PMCID: PMC9831608 DOI: 10.7554/elife.79765] [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: 04/25/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The circadian clock governs rhythmic cellular functions by driving the expression of a substantial fraction of the genome and thereby significantly contributes to the adaptation to changing environmental conditions. Using the circadian model organism Neurospora crassa, we show that molecular timekeeping is robust even under severe limitation of carbon sources, however, stoichiometry, phosphorylation and subcellular distribution of the key clock components display drastic alterations. Protein kinase A, protein phosphatase 2 A and glycogen synthase kinase are involved in the molecular reorganization of the clock. RNA-seq analysis reveals that the transcriptomic response of metabolism to starvation is highly dependent on the positive clock component WC-1. Moreover, our molecular and phenotypic data indicate that a functional clock facilitates recovery from starvation. We suggest that the molecular clock is a flexible network that allows the organism to maintain rhythmic physiology and preserve fitness even under long-term nutritional stress.
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Affiliation(s)
- Anita Szőke
- Department of Physiology, Semmelweis UniversityBudapestHungary
| | - Orsolya Sárkány
- Department of Physiology, Semmelweis UniversityBudapestHungary
| | - Géza Schermann
- Department of Neurovascular Cellbiology, University Hospital BonnBonnGermany
| | - Orsolya Kapuy
- Department of Molecular Biology, Semmelweis UniversityBudapestHungary
| | | | | | - Norbert Gyöngyösi
- Department of Molecular Biology, Semmelweis UniversityBudapestHungary
| | - Krisztina Káldi
- Department of Physiology, Semmelweis UniversityBudapestHungary
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10
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Castillo KD, Wu C, Ding Z, Lopez-Garcia OK, Rowlinson E, Sachs MS, Bell-Pedersen D. A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules. Cell Rep 2022; 41:111879. [PMID: 36577368 PMCID: PMC10241597 DOI: 10.1016/j.celrep.2022.111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/13/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.
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Affiliation(s)
- Kathrina D Castillo
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Zhaolan Ding
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Emma Rowlinson
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Deborah Bell-Pedersen
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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11
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Galasso L, Calogiuri G, Castelli L, Mulè A, Esposito F, Caumo A, Montaruli A, Roveda E. Theoretical construct into blocks of actigraphic-derived sleep parameters. Chronobiol Int 2022; 40:174-185. [PMID: 36530154 DOI: 10.1080/07420528.2022.2157737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Actigraphic parameters can provide indication of people's sleep quality during their daily lives. However, there is a need for clear guidelines on the understanding of the different actigraphic parameters. The present study aims to propose a conceptual and theoretical framework for known actigraphic-derived parameters, which is able to describe the alternation between rest and wake phases during the nocturnal sleep, explaining their main characteristics and interrelations that can be replicated in future studies. Forty Sport Sciences students at the University of Milan (20 males; mean age ± SD, 22 ± 3 y) completed the validated Italian version of Morningness-Eveningness Questionnaire (MEQ) and wore an actigraph (Motion Watch 8®, Cambridge Neurotechnology, Cambridge, UK) for seven days. A framework was developed to depict the interactions between the actigraphic parameters and how they objectively describe sleep, according to which the parameters are organized into three different functional blocks related to different aspects of sleep. Correlations analyses were conducted to explore the relationships among the primary actigraphic parameters within and across the functional blocks. The proposed framework is a purely theoretical construct that provides a simple interpretation of known actigraphic parameters guiding researchers and practitioners in the use of these parameters either for research or clinical purposes.
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Affiliation(s)
- Letizia Galasso
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Giovanna Calogiuri
- Center for Health and Technology, Department of Nursing and Health Sciences, Faculty of Health and Social Sciences, University of South-Eastern Norway, Drammen, Norway
- Department of Public Health and Sport Sciences, Faculty of Health and Social Sciences, Inland Norway University of Applied Sciences, Elverum, Norway
| | - Lucia Castelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Antonino Mulè
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Fabio Esposito
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Andrea Caumo
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Angela Montaruli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Eliana Roveda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
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12
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The role of spatiotemporal organization and dynamics of clock complexes in circadian regulation. Curr Opin Cell Biol 2022; 78:102129. [PMID: 36126370 DOI: 10.1016/j.ceb.2022.102129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/26/2022] [Accepted: 08/19/2022] [Indexed: 01/31/2023]
Abstract
Circadian clocks are cell autonomous timekeepers that regulate ∼24-h oscillations in the expression of many genes and control rhythms in nearly all our behavior and physiology. Almost every cell in the human body has a molecular clock and networks of cells containing clock proteins orchestrate daily rhythms in many physiological processes, from sleep-wake cycles to metabolism to immunity. All eukaryotic circadian clocks are based on transcription-translation delayed negative feedback loops in which activation of core clock genes is negatively regulated by their cognate protein products. Our current understanding of circadian clocks has been accumulated from decades of genetic and biochemical experiments, however, what remains poorly understood is how clock proteins, genes, and mRNAs are spatiotemporally organized within live clock cells and how such subcellular organization affects circadian rhythms at the single cell level. Here, we review recent progress in understanding how clock proteins and genes are spatially organized within clock cells over the circadian cycle and the role of such organization in generating circadian rhythms and highlight open questions for future studies.
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13
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Singh A, Li C, Diernfellner ACR, Höfer T, Brunner M. Data-driven modelling captures dynamics of the circadian clock of Neurospora crassa. PLoS Comput Biol 2022; 18:e1010331. [PMID: 35951637 PMCID: PMC9397904 DOI: 10.1371/journal.pcbi.1010331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/23/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic circadian clocks are based on self-sustaining, cell-autonomous oscillatory feedback loops that can synchronize with the environment via recurrent stimuli (zeitgebers) such as light. The components of biological clocks and their network interactions are becoming increasingly known, calling for a quantitative understanding of their role for clock function. However, the development of data-driven mathematical clock models has remained limited by the lack of sufficiently accurate data. Here we present a comprehensive model of the circadian clock of Neurospora crassa that describe free-running oscillations in constant darkness and entrainment in light-dark cycles. To parameterize the model, we measured high-resolution time courses of luciferase reporters of morning and evening specific clock genes in WT and a mutant strain. Fitting the model to such comprehensive data allowed estimating parameters governing circadian phase, period length and amplitude, and the response of genes to light cues. Our model suggests that functional maturation of the core clock protein Frequency causes a delay in negative feedback that is critical for generating circadian rhythms. Circadian rhythms are endogenous autonomous clocks that emancipate daily rhythms in physiology and behavior. Lately, a large body of research has contributed to our understanding of clocks’ genetic and mechanistic basis across kingdoms of life, i.e., mammals, fungi, plants, and bacteria. Several mathematical models have made key contributions to our current understanding of the design principles of the Neurospora crassa circadian clock and conditions for self-sustained oscillations. However, previous models uncovered and described the principle properties of the clock in generic manner due to a lack of experimental data. In this study, we developed a mathematical model based on systems of differential equations to describe the core clock components and estimated model parameters from luciferase data that capture experimental observations. We demonstrate the model predictive control simulation emphasizing the importance of functional maturation of the core clock protein Frequency in generating circadian rhythms.
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Affiliation(s)
- Amit Singh
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Congxin Li
- Theoretical Systems Biology [B086] Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | | | - Thomas Höfer
- Theoretical Systems Biology [B086] Deutsches Krebsforschungszentrum, Heidelberg, Germany
- * E-mail: (TH); (MB)
| | - Michael Brunner
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- * E-mail: (TH); (MB)
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14
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Burt P, Grabe S, Madeti C, Upadhyay A, Merrow M, Roenneberg T, Herzel H, Schmal C. Principles underlying the complex dynamics of temperature entrainment by a circadian clock. iScience 2021; 24:103370. [PMID: 34816105 PMCID: PMC8593569 DOI: 10.1016/j.isci.2021.103370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/01/2021] [Accepted: 10/25/2021] [Indexed: 01/20/2023] Open
Abstract
Autonomously oscillating circadian clocks resonate with daily environmental (zeitgeber) rhythms to organize physiology around the solar day. Although entrainment properties and mechanisms have been studied widely and in great detail for light-dark cycles, entrainment to daily temperature rhythms remains poorly understood despite that they are potent zeitgebers. Here we investigate the entrainment of the chronobiological model organism Neurospora crassa, subject to thermocycles of different periods and fractions of warm versus cold phases, mimicking seasonal variations. Depending on the properties of these thermocycles, regularly entrained rhythms, period-doubling (frequency demultiplication) but also irregular aperiodic behavior occurs. We demonstrate that the complex nonlinear phenomena of experimentally observed entrainment dynamics can be understood by molecular mathematical modeling.
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Affiliation(s)
- Philipp Burt
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Saskia Grabe
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Cornelia Madeti
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Abhishek Upadhyay
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Martha Merrow
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Till Roenneberg
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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15
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From circadian clock mechanism to sleep disorders and jet lag: Insights from a computational approach. Biochem Pharmacol 2021; 191:114482. [DOI: 10.1016/j.bcp.2021.114482] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
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16
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Cellular Calcium Levels Influenced by NCA-2 Impact Circadian Period Determination in Neurospora. mBio 2021; 12:e0149321. [PMID: 34182778 PMCID: PMC8262947 DOI: 10.1128/mbio.01493-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intracellular calcium signaling has been implicated in the control of a variety of circadian processes in animals and plants, but its role in microbial clocks has remained largely cryptic. To examine the role of intracellular Ca2+ in the Neurospora clock, we screened mutants with knockouts of calcium transporter genes and identified a gene encoding a calcium exporter, nca-2, uniquely as having significant period effects. The loss of NCA-2 results in an increase in the cytosolic calcium level, and this leads to hyper-phosphorylation of core clock components, FRQ and WC-1, and a short period, as measured by both the core oscillator and the overt clock. Genetic analyses showed that mutations in certain frq phospho-sites and in Ca2+-calmodulin-dependent kinase 2 (camk-2) are epistatic to nca-2 in controlling the pace of the oscillator. These data are consistent with a model in which elevated intracellular Ca2+ leads to the increased activity of CAMK-2, leading to enhanced FRQ phosphorylation, accelerated closure of the circadian feedback loop, and a shortened circadian period length. At a mechanistic level, some CAMKs undergo more auto-phosphorylations in the Δnca-2 mutant, consistent with high calcium levels in the Δnca-2 mutant influencing the enzymatic activities of CAMKs. NCA-2 interacts with multiple proteins, including CSP-6, a protein known to be required for circadian output. Most importantly, the expression of nca-2 is circadian clock-controlled at both the transcriptional and translational levels, and this in combination with the period effects seen in strains lacking NCA-2 firmly places calcium signaling within the larger circadian system, where it acts as both an input to and an output from the core clock.
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17
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Ahmad SF, Shanaz S, Kumar A, Dar AH, Mohmad A, Bhushan B. Crosstalk of epigenetics with biological rhythmicity in animal kingdom. BIOL RHYTHM RES 2021. [DOI: 10.1080/09291016.2019.1607218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Syed Shanaz
- Department of Animal Genetics and Breeding, Sher-i-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Abhishek Kumar
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Aashaq Hussain Dar
- Department of Livestock Production and Management, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand
| | - Aquil Mohmad
- Division of Parasitology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
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18
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Rosbash M. Circadian Rhythms and the Transcriptional Feedback Loop (Nobel Lecture)**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Rosbash
- Department of Biology Howard Hughes Medical Institute Brandeis University Waltham MA USA
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19
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Rosbash M. Circadian Rhythms and the Transcriptional Feedback Loop (Nobel Lecture)**. Angew Chem Int Ed Engl 2021; 60:8650-8666. [DOI: 10.1002/anie.202015199] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Rosbash
- Department of Biology Howard Hughes Medical Institute Brandeis University Waltham MA USA
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20
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Srikanta SB, Cermakian N. To Ub or not to Ub: Regulation of circadian clocks by ubiquitination and deubiquitination. J Neurochem 2020; 157:11-30. [PMID: 32717140 DOI: 10.1111/jnc.15132] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/28/2022]
Abstract
Circadian clocks are internal timing systems that enable organisms to adjust their behavioral and physiological rhythms to the daily changes of their environment. These clocks generate self-sustained oscillations at the cellular, tissue, and behavioral level. The rhythm-generating mechanism is based on a gene expression network with a delayed negative feedback loop that causes the transcripts to oscillate with a period of approximately 24 hr. This oscillatory nature of the proteins involved in this network necessitates that they are intrinsically unstable, with a short half-life. Hence, post-translational modifications (PTMs) are important to precisely time the presence, absence, and interactions of these proteins at appropriate times of the day. Ubiquitination and deubiquitination are counter-balancing PTMs which play a key role in this regulatory process. In this review, we take a comprehensive look at the roles played by the processes of ubiquitination and deubiquitination in the clock machinery of the most commonly studied eukaryotic models of the circadian clock: plants, fungi, fruit flies, and mammals. We present the effects exerted by ubiquitinating and deubiquitinating enzymes on the stability, but also the activity, localization, and interactions of clock proteins. Overall, these PTMs have key roles in regulating not only the pace of the circadian clocks but also their response to external cues and their control of cellular functions.
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Affiliation(s)
- Shashank Bangalore Srikanta
- Integrated Program in Neuroscience, McGill University, Montréal, QC, Canada.,Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada
| | - Nicolas Cermakian
- Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada.,Department of Psychiatry, McGill University, Montréal, QC, Canada
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21
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Abstract
In Neurospora and other fungi, the protein frequency (FRQ) is an integral part and a negative element in the fungal circadian oscillator. In Drosophila and many other higher organisms, the protein period (PER) is an integral part and a negative element of their circadian oscillator. Employing bioinformatic techniques, such as BLAST, CLUSTAL, and MEME (Multiple Em for Motif Elicitation), 11 regions (sequences) of potential similarity were found between the fungal FRQ and the Drosophila PER. Many of these FRQ regions are conserved in many fungal FRQ(s). Many of these PER regions are conserved in many insects. In addition, these regions are also of biological significance since mutations in these regions lead to changes in the circadian clock of Neurospora and Drosophila. Many of these regions of similarity between FRQ and PER are also conserved between the Drosophila PER and the mouse PER (mPER2). This suggests conserved and important regions for all 3 proteins and a common ancestor, possibly in those amoeba, such as Capsaspora, that sits at the base of the phylogenetic tree where fungi and animals diverged. Two additional examples of a possible common ancestor between Neurospora and Drosophila were found. One, the white collar (WC-1) protein of Neurospora and the Drosophila PER, shows significant similarity in its Per/Arnt/Sim (PAS) motifs to the PAS motif of an ARNT-like protein found in the amoeba, Capsaspora. Two, both of the positive elements in each system (i.e., WC-1 in Neurospora and cycle [CYC] in Drosophila), show significant similarity to this Capsaspora ARNT protein. A discussion of these findings centers on the long-time debate about the origins of the many different clock systems (i.e., independent evolution or common ancestor as well as to the question of how new genes are formed).
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Affiliation(s)
- Stuart Brody
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, and Center for Circadian Biology, UCSD, La Jolla, California
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22
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Lee B, Shin D, Gross SP, Cho KH. Combined Positive and Negative Feedback Allows Modulation of Neuronal Oscillation Frequency during Sensory Processing. Cell Rep 2019; 25:1548-1560.e3. [PMID: 30404009 DOI: 10.1016/j.celrep.2018.10.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/21/2018] [Accepted: 10/03/2018] [Indexed: 10/27/2022] Open
Abstract
A key step in sensory information processing involves modulation and integration of neuronal oscillations in disparate frequency bands, a poorly understood process. Here, we investigate how top-down input causes frequency changes in slow oscillations during sensory processing and, in turn, how the slow oscillations are combined with fast oscillations (which encode sensory input). Using experimental connectivity patterns and strengths of interneurons, we develop a system-level model of a neuronal circuit controlling these oscillatory behaviors, allowing us to understand the mechanisms responsible for the observed oscillatory behaviors. Our analysis discovers a circuit capable of producing the observed oscillatory behaviors and finds that a detailed balance in the strength of synaptic connections is the critical determinant to produce such oscillatory behaviors. We not only uncover how disparate frequency bands are modulated and combined but also give insights into the causes of abnormal neuronal activities present in brain disorders.
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Affiliation(s)
- Byeongwook Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Dongkwan Shin
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Steven P Gross
- Department of Developmental and Cell Biology, UC Irvine, Irvine, CA 92697, USA
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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23
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Nieto PS, Condat CA. Translational thresholds in a core circadian clock model. Phys Rev E 2019; 100:022409. [PMID: 31574627 DOI: 10.1103/physreve.100.022409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 06/10/2023]
Abstract
Organisms have evolved in a daily cyclic environment, developing circadian cell-autonomous clocks that temporally organize a wide range of biological processes. Translation is a highly regulated process mainly associated with the activity of microRNAs (miRNAs) at the translation initiation step that impacts on the molecular circadian clock dynamics. Recently, a molecular titration mechanism was proposed to explain the interactions between some miRNAs and their target mRNAs; new evidence also indicates that regulation by miRNA is a nonlinear process such that there is a threshold level of target mRNA below which protein production is drastically repressed. These observations led us to use a theoretical model of the circadian molecular clock to study the effect of miRNA-mediated translational thresholds on the molecular clock dynamics. We model the translational threshold by introducing a phenomenological Hill equation for the kinetics of PER translation and show how the parameters associated with translation kinetics affect the period, amplitude, and time delays between clock mRNA and clock protein expression. We show that our results are useful for analyzing experiments related to the translational regulation of negative elements of transcriptional-translational feedback loops. We also provide new elements for thinking about the translational threshold as a mechanism that favors the emergence of circadian rhythmicity, the tuning of the period-delay relationship and the cell capacity to control the protein oscillation amplitude with almost negligible changes in the mRNA amplitudes.
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Affiliation(s)
- Paula S Nieto
- Instituto de Física Enrique Gaviola (IFEG)-CONICET and Facultad de Matemática, Astronomía, Física y Computación, Universidad Nacional de Córdoba, Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
| | - C A Condat
- Instituto de Física Enrique Gaviola (IFEG)-CONICET and Facultad de Matemática, Astronomía, Física y Computación, Universidad Nacional de Córdoba, Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
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24
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Upadhyay A, Brunner M, Herzel H. An Inactivation Switch Enables Rhythms in a Neurospora Clock Model. Int J Mol Sci 2019; 20:E2985. [PMID: 31248072 PMCID: PMC6627049 DOI: 10.3390/ijms20122985] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 12/17/2022] Open
Abstract
Autonomous endogenous time-keeping is ubiquitous across many living organisms, known as the circadian clock when it has a period of about 24 h. Interestingly, the fundamental design principle with a network of interconnected negative and positive feedback loops is conserved through evolution, although the molecular components differ. Filamentous fungus Neurospora crassa is a well-established chrono-genetics model organism to investigate the underlying mechanisms. The core negative feedback loop of the clock of Neurospora is composed of the transcription activator White Collar Complex (WCC) (heterodimer of WC1 and WC2) and the inhibitory element called FFC complex, which is made of FRQ (Frequency protein), FRH (Frequency interacting RNA Helicase) and CK1a (Casein kinase 1a). While exploring their temporal dynamics, we investigate how limit cycle oscillations arise and how molecular switches support self-sustained rhythms. We develop a mathematical model of 10 variables with 26 parameters to understand the interactions and feedback among WC1 and FFC elements in nuclear and cytoplasmic compartments. We performed control and bifurcation analysis to show that our novel model produces robust oscillations with a wild-type period of 22.5 h. Our model reveals a switch between WC1-induced transcription and FFC-assisted inactivation of WC1. Using the new model, we also study the possible mechanisms of glucose compensation. A fairly simple model with just three nonlinearities helps to elucidate clock dynamics, revealing a mechanism of rhythms' production. The model can further be utilized to study entrainment and temperature compensation.
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Affiliation(s)
- Abhishek Upadhyay
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin and Humboldt University of Berlin, Philippstr. 13, 10115 Berlin, Germany.
| | - Michael Brunner
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin and Humboldt University of Berlin, Philippstr. 13, 10115 Berlin, Germany.
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25
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Cao Z, Grima R. Accuracy of parameter estimation for auto-regulatory transcriptional feedback loops from noisy data. J R Soc Interface 2019; 16:20180967. [PMID: 30940028 PMCID: PMC6505555 DOI: 10.1098/rsif.2018.0967] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bayesian and non-Bayesian moment-based inference methods are commonly used to estimate the parameters defining stochastic models of gene regulatory networks from noisy single cell or population snapshot data. However, a systematic investigation of the accuracy of the predictions of these methods remains missing. Here, we present the results of such a study using synthetic noisy data of a negative auto-regulatory transcriptional feedback loop, one of the most common building blocks of complex gene regulatory networks. We study the error in parameter estimation as a function of (i) number of cells in each sample; (ii) the number of time points; (iii) the highest-order moment of protein fluctuations used for inference; (iv) the moment-closure method used for likelihood approximation. We find that for sample sizes typical of flow cytometry experiments, parameter estimation by maximizing the likelihood is as accurate as using Bayesian methods but with a much reduced computational time. We also show that the choice of moment-closure method is the crucial factor determining the maximum achievable accuracy of moment-based inference methods. Common likelihood approximation methods based on the linear noise approximation or the zero cumulants closure perform poorly for feedback loops with large protein-DNA binding rates or large protein bursts; this is exacerbated for highly heterogeneous cell populations. By contrast, approximating the likelihood using the linear-mapping approximation or conditional derivative matching leads to highly accurate parameter estimates for a wide range of conditions.
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26
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Abstract
Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components. Posttranslational modifications and protein–protein interactions have become a recent focus, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. This review covers the structural aspects of circadian oscillators, and serves as a primer for this exciting realm of structural biology.
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Affiliation(s)
- Reena Saini
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Seth J Davis
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany. .,Department of Biology, University of York, York, UK.
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27
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Maywood ES. Synchronization and maintenance of circadian timing in the mammalian clockwork. Eur J Neurosci 2018; 51:229-240. [DOI: 10.1111/ejn.14279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/19/2018] [Accepted: 10/30/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Elizabeth S. Maywood
- Neurobiology DivisionMedical Research Council Laboratory of Molecular Biology Cambridge UK
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28
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Modeling the crosstalk between the circadian clock and ROS in Neurospora crassa. J Theor Biol 2018; 458:125-132. [DOI: 10.1016/j.jtbi.2018.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/19/2018] [Accepted: 09/13/2018] [Indexed: 11/18/2022]
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29
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Wang LS, Li NX, Chen JJ, Zhang XP, Liu F, Wang W. Modulation of dynamic modes by interplay between positive and negative feedback loops in gene regulatory networks. Phys Rev E 2018; 97:042412. [PMID: 29758769 DOI: 10.1103/physreve.97.042412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Indexed: 11/07/2022]
Abstract
A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops. We developed an abstract model of such systems, largely based on the core p53 pathway, to explore the mechanism for the transformation of dynamic behaviors. Our results show that enhancing the positive feedback may promote or suppress oscillations depending on the strength of both feedback loops. We found that the system oscillates with low amplitudes in response to a moderate stimulus and switches to the on state upon a strong stimulus. When the positive feedback is activated much later than the negative one in response to a strong stimulus, the system exhibits long-term oscillations before switching to the on state. We explain this intriguing phenomenon using quasistatic approximation. Moreover, early switching to the on state may occur when the system starts from a steady state in the absence of stimuli. The interplay between the positive and negative feedback plays a key role in the transitions between oscillation and bistability. Of note, our conclusions should be applicable only to some specific gene regulatory networks, especially the p53 network, in which both oscillation and bistability exist in response to a certain type of stimulus. Our work also underscores the significance of transient dynamics in determining cellular outcome.
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Affiliation(s)
- Liu-Suo Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China.,National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Ning-Xi Li
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jing-Jia Chen
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Xiao-Peng Zhang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China.,National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Feng Liu
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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30
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Joanito I, Chu JW, Wu SH, Hsu CP. An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states. Sci Rep 2018; 8:13944. [PMID: 30224713 PMCID: PMC6141573 DOI: 10.1038/s41598-018-32030-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
In higher plants (e.g., Arabidopsis thaliana), the core structure of the circadian clock is mostly governed by a repression process with very few direct activators. With a series of simplified models, we studied the underlying mechanism and found that the Arabidopsis clock consists of type-2 incoherent feed-forward loops (IFFLs), one of them creating a pulse-like expression in PRR9/7. The double-negative feedback loop between CCA1/LHY and PRR5/TOC1 generates a bistable, hysteretic behavior in the Arabidopsis circadian clock. We found that the IFFL involving PRR9/7 breaks the bistability and moves the system forward with a rapid pulse in the daytime, and the evening complex (EC) breaks it in the evening. With this illustration, we can intuitively explain the behavior of the clock under mutant conditions. Thus, our results provide new insights into the underlying network structures of the Arabidopsis core oscillator.
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Affiliation(s)
- Ignasius Joanito
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Jhih-Wei Chu
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.
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31
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Modeling Reveals a Key Mechanism for Light-Dependent Phase Shifts of Neurospora Circadian Rhythms. Biophys J 2018; 115:1093-1102. [PMID: 30139524 DOI: 10.1016/j.bpj.2018.07.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/11/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
Light shifts and synchronizes the phase of the circadian clock to daily environments, which is critical for maintaining the daily activities of an organism. It has been proposed that such light-dependent phase shifts are triggered by light-induced upregulation of a negative element of the core circadian clock (i.e., frq, Per1/2) in many organisms, including fungi. However, we find, using systematic mathematical modeling of the Neurospora crassa circadian clock, that the upregulation of the frq gene expression alone is unable to reproduce the observed light-dependent phase responses. Indeed, we find that the depression of the transcriptional activator white-collar-1, previously shown to be promoted by FRQ and VVD, is a key molecular mechanism for accurately simulating light-induced phase response curves for wild-type and mutant strains of Neurospora. Our findings elucidate specific molecular pathways that can be utilized to control phase resetting of circadian rhythms.
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32
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Guan Y, Li Z, Wang S, Barnes PM, Liu X, Xu H, Jin M, Liu AP, Yang Q. A robust and tunable mitotic oscillator in artificial cells. eLife 2018; 7:33549. [PMID: 29620527 PMCID: PMC5922972 DOI: 10.7554/elife.33549] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/04/2018] [Indexed: 11/16/2022] Open
Abstract
Single-cell analysis is pivotal to deciphering complex phenomena like heterogeneity, bistability, and asynchronous oscillations, where a population ensemble cannot represent individual behaviors. Bulk cell-free systems, despite having unique advantages of manipulation and characterization of biochemical networks, lack the essential single-cell information to understand a class of out-of-steady-state dynamics including cell cycles. Here, by encapsulating Xenopus egg extracts in water-in-oil microemulsions, we developed artificial cells that are adjustable in sizes and periods, sustain mitotic oscillations for over 30 cycles, and function in forms from the simplest cytoplasmic-only to the more complicated ones involving nuclear dynamics, mimicking real cells. Such innate flexibility and robustness make it key to studying clock properties like tunability and stochasticity. Our results also highlight energy as an important regulator of cell cycles. We demonstrate a simple, powerful, and likely generalizable strategy of integrating strengths of single-cell approaches into conventional in vitro systems to study complex clock functions.
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Affiliation(s)
- Ye Guan
- Department of Biophysics, University of Michigan, Ann Arbor, United States.,Department of Chemistry, University of Michigan, Ann Arbor, United States
| | - Zhengda Li
- Department of Biophysics, University of Michigan, Ann Arbor, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Shiyuan Wang
- Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Patrick M Barnes
- Department of Physics, University of Michigan, Ann Arbor, United States
| | - Xuwen Liu
- Department of Physics, University of Science and Technology of China, Hefei Shi, China
| | - Haotian Xu
- Department of Computer Science, Wayne State University, Detroit, United States
| | - Minjun Jin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Allen P Liu
- Department of Biophysics, University of Michigan, Ann Arbor, United States.,Department of Mechanical Engineering, University of Michigan, Ann Arbor, United States
| | - Qiong Yang
- Department of Biophysics, University of Michigan, Ann Arbor, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States.,Department of Physics, University of Michigan, Ann Arbor, United States
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33
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Dunlap JC, Loros JJ. Just-So Stories and Origin Myths: Phosphorylation and Structural Disorder in Circadian Clock Proteins. Mol Cell 2017; 69:165-168. [PMID: 29276084 DOI: 10.1016/j.molcel.2017.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/19/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022]
Abstract
Some longstanding dogmas in the circadian field warrant reexamination in light of recent studies focused on the role of post-translational modifications and intrinsic disorder in core circadian clock proteins of mice and fungi. Such dogmas include the role of turnover in circadian feedback loops and the origin myths describing evolutionary relatedness among circadian clocks. In this Essay, the authors recapitulate recent findings on circadian clock protein regulation by taking an unconventional approach in the form of a dialog between Wizard and Apprentice.
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Affiliation(s)
- Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755.
| | - Jennifer J Loros
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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34
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Stevenson TJ. Epigenetic Regulation of Biological Rhythms: An Evolutionary Ancient Molecular Timer. Trends Genet 2017; 34:90-100. [PMID: 29221677 DOI: 10.1016/j.tig.2017.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 01/12/2023]
Abstract
Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, I propose an epigenetic clock model that outlines how molecular modifications, such as DNA methylation, are integral components for timing endogenous biological rhythms. The hypothesis proposed is that an epigenetic clock serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells, from unicellular to complex organisms. The model also provides a novel framework for the timing of epigenetic modifications during the lifespan and transgenerational inheritance of an organism.
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Affiliation(s)
- Tyler J Stevenson
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
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35
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de Bekker C, Will I, Hughes DP, Brachmann A, Merrow M. Daily rhythms and enrichment patterns in the transcriptome of the behavior-manipulating parasite Ophiocordyceps kimflemingiae. PLoS One 2017; 12:e0187170. [PMID: 29099875 PMCID: PMC5669440 DOI: 10.1371/journal.pone.0187170] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/13/2017] [Indexed: 12/22/2022] Open
Abstract
Various parasite-host interactions that involve adaptive manipulation of host behavior display time-of-day synchronization of certain events. One example is the manipulated biting behavior observed in Carpenter ants infected with Ophiocordyceps unilateralis sensu lato. We hypothesized that biological clocks play an important role in this and other parasite-host interactions. In order to identify candidate molecular clock components, we used two general strategies: bioinformatics and transcriptional profiling. The bioinformatics approach was used to identify putative homologs of known clock genes. For transcriptional profiling, RNA-Seq was performed on 48 h time courses of Ophiocordyceps kimflemingiae (a recently named species of the O. unilateralis complex), whose genome has recently been sequenced. Fungal blastospores were entrained in liquid media under 24 h light-dark (LD) cycles and were harvested at 4 h intervals either under LD or continuous darkness. Of all O. kimflemingiae genes, 5.3% had rhythmic mRNAs under these conditions (JTK Cycle, ≤ 0.057 statistical cutoff). Our data further indicates that a significant number of transcription factors have a peaked activity during the light phase (day time). The expression levels of a significant number of secreted enzymes, proteases, toxins and small bioactive compounds peaked during the dark phase or subjective night. These findings support a model whereby this fungal parasite uses its biological clock for phase-specific activity. We further suggest that this may be a general mechanism involved in parasite-host interactions.
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Affiliation(s)
- Charissa de Bekker
- University of Central Florida, Department of Biology, Orlando, Florida, United States of America
- LMU Munich, Institute of Medical Psychology, Faculty of Medicine, Munich, Germany
- LMU Munich, Genetics, Faculty of Biology, Planegg-Martinsried, Germany
- * E-mail:
| | - Ian Will
- University of Central Florida, Department of Biology, Orlando, Florida, United States of America
- LMU Munich, Institute of Medical Psychology, Faculty of Medicine, Munich, Germany
| | - David P. Hughes
- Pennsylvania State University, Departments of Biology and Entomology, University Park, Pennsylvania, United States of America
| | - Andreas Brachmann
- LMU Munich, Genetics, Faculty of Biology, Planegg-Martinsried, Germany
| | - Martha Merrow
- LMU Munich, Institute of Medical Psychology, Faculty of Medicine, Munich, Germany
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36
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Koritala BSC, Lee K. Natural Variation of the Circadian Clock in Neurospora. ADVANCES IN GENETICS 2017; 99:1-37. [PMID: 29050553 DOI: 10.1016/bs.adgen.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most living organisms on earth experience daily and expected changes from the rotation of the earth. For an organism, the ability to predict and prepare for incoming stresses or resources is a very important skill for survival. This cellular process of measuring daily time of the day is collectively called the circadian clock. Because of its fundamental role in survival in nature, there is a great interest in studying the natural variation of the circadian clock. However, characterizing the genetic and molecular mechanisms underlying natural variation of circadian clocks remains a challenging task. In this chapter, we will summarize the progress in studying natural variation of the circadian clock in the successful eukaryotic model Neurospora, which led to discovering many design principles of the molecular mechanisms of the eukaryotic circadian clock. Despite the success of the system in revealing the molecular mechanisms of the circadian clock, Neurospora has not been utilized to extensively study natural variation. We will review the challenges that hindered the natural variation studies in Neurospora, and how they were overcome. We will also review the advantages of Neurospora for natural variation studies. Since Neurospora is the model fungal species for circadian study, it represents over 5 million species of fungi on earth. These fungi play important roles in ecosystems on earth, and as such Neurospora could serve as an important model for understanding the ecological role of natural variation in fungal circadian clocks.
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Affiliation(s)
- Bala S C Koritala
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States
| | - Kwangwon Lee
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States.
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37
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Gyöngyösi N, Szőke A, Ella K, Káldi K. The small G protein RAS2 is involved in the metabolic compensation of the circadian clock in the circadian model Neurospora crassa. J Biol Chem 2017; 292:14929-14939. [PMID: 28729421 DOI: 10.1074/jbc.m117.804922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence from both experimental and clinical investigations indicates a tight interaction between metabolism and circadian timekeeping; however, knowledge of the underlying mechanism is still incomplete. Metabolic compensation allows circadian oscillators to run with a constant speed at different substrate levels and, therefore, is a substantial criterion of a robust rhythm in a changing environment. Because previous data have suggested a central role of RAS2-mediated signaling in the adaptation of yeast to different nutritional environments, we examined the involvement of RAS2 in the metabolic regulation of the clock in the circadian model organism Neurospora crassa We show that, in a ras2-deficient strain, the period is longer than in the control. Moreover, unlike in the WT, in Δras2, operation of the circadian clock was affected by glucose; compared with starvation conditions, the period was longer and the oscillation of expression of the frequency (frq) gene was dampened. In constant darkness, the delayed phosphorylation of the FRQ protein and the long-lasting accumulation of FRQ in the nucleus were in accordance with the longer period and the less robust rhythm in the mutant. Although glucose did not affect the subcellular distribution of FRQ in the WT, highly elevated FRQ levels were detected in the nucleus in Δras2 RAS2 interacted with the RAS-binding domain of the adenylate cyclase in vitro, and the cAMP analogue 8-bromo-cyclic AMP partially rescued the circadian phenotype in vivo We therefore propose that RAS2 acts via a cAMP-dependent pathway and exerts significant metabolic control on the Neurospora circadian clock.
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Affiliation(s)
- Norbert Gyöngyösi
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
| | - Anita Szőke
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
| | - Krisztina Ella
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
| | - Krisztina Káldi
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
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38
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Fanelli F, Reveglia P, Masi M, Mulè G, Zonno MC, Cimmino A, Vurro M, Evidente A. Influence of light on the biosynthesis of ophiobolin A by Bipolaris maydis. Nat Prod Res 2016; 31:909-917. [PMID: 27820961 DOI: 10.1080/14786419.2016.1253084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ophiobolin A (O-A) is a sesterpenoid with numerous biological activities, including potential anticancer effects. Its production at an industrial level is hampered due to inability of fungus Bipolaris maydis to biosynthesise it in vitro in large amount. Among the environmental factors regulating fungal metabolism, light plays a crucial role. In this study, the use of different light wavelength (light emitting diodes (LEDs)) was evaluated to increase the O-A production. The white light allowed the highest production of the metabolite. The blue and green lights showed an inhibitory effect, reducing the production to 50%, as well as red and yellow but at a lower level. No correlation between fungal growth and metabolite production was found in relation to the light type. A novel application of LED technologies, which can be optimised to foster specific pathways and promote the production of metabolites having scientific and industrial interest was proposed.
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Affiliation(s)
- Francesca Fanelli
- a Institute of Sciences of Food Production , National Research Council , Bari , Italy
| | - Pierluigi Reveglia
- b Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Napoli , Italy
| | - Marco Masi
- b Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Napoli , Italy
| | - Giuseppina Mulè
- a Institute of Sciences of Food Production , National Research Council , Bari , Italy
| | - Maria Chiara Zonno
- a Institute of Sciences of Food Production , National Research Council , Bari , Italy
| | - Alessio Cimmino
- b Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Napoli , Italy
| | - Maurizio Vurro
- a Institute of Sciences of Food Production , National Research Council , Bari , Italy
| | - Antonio Evidente
- b Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Napoli , Italy
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39
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Huang B, Tian X, Liu F, Wang W. Impact of time delays on oscillatory dynamics of interlinked positive and negative feedback loops. Phys Rev E 2016; 94:052413. [PMID: 27967134 DOI: 10.1103/physreve.94.052413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Interlinking a positive feedback loop (PFL) with a negative feedback loop (NFL) constitutes a typical motif in genetic networks, performing various functions in cell signaling. How time delay in feedback regulation affects the dynamics of such systems still remains unclear. Here, we investigate three systems of interlinked PFL and NFL with time delays: a synthetic genetic oscillator, a three-node circuit, and a simplified single-node model. The stability of steady states and the routes to oscillation in the single-node model are analyzed in detail. The amplitude and period of oscillations vary with a pointwise periodicity over a range of time delay. Larger-amplitude oscillations can be induced when the PFL has an appropriately long delay, in comparison with the PFL with no delay or short delay; this conclusion holds true for all the three systems. We unravel the underlying mechanism for the above effects via analytical derivation under a limiting condition. We also develop a stochastic algorithm for simulating a single reaction with two delays and show that robust oscillations can be maintained by the PFL with a properly long delay in the single-node system. This work presents an effective method for constructing robust large-amplitude oscillators and interprets why similar circuit architectures are engaged in timekeeping systems such as circadian clocks.
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Affiliation(s)
- Bo Huang
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Xinyu Tian
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Feng Liu
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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40
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Hurley JM, Loros JJ, Dunlap JC. Circadian Oscillators: Around the Transcription-Translation Feedback Loop and on to Output. Trends Biochem Sci 2016; 41:834-846. [PMID: 27498225 DOI: 10.1016/j.tibs.2016.07.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/10/2016] [Accepted: 07/14/2016] [Indexed: 12/20/2022]
Abstract
From cyanobacteria to mammals, organisms have evolved timing mechanisms to adapt to environmental changes in order to optimize survival and improve fitness. To anticipate these regular daily cycles, many organisms manifest ∼24h cell-autonomous oscillations that are sustained by transcription-translation-based or post-transcriptional negative-feedback loops that control a wide range of biological processes. With an eye to identifying emerging common themes among cyanobacterial, fungal, and animal clocks, some major recent developments in the understanding of the mechanisms that regulate these oscillators and their output are discussed. These include roles for antisense transcription, intrinsically disordered proteins, codon bias in clock genes, and a more focused discussion of post-transcriptional and translational regulation as a part of both the oscillator and output.
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Affiliation(s)
- Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Jennifer J Loros
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
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41
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Abstract
In considering the impact of the earth’s changing geophysical conditions during the history of life, it is surprising to learn that the earth’s rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago). The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the “protoclock” in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished. They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences. They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving. In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization.
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Affiliation(s)
- Eran Tauber
- Department of Genetics, University of Leicester, Leicester, UK
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42
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de Paula RM, Lewis ZA, Greene AV, Seo KS, Morgan LW, Vitalini MW, Bennett L, Gomer RH, Bell-Pedersen D. Two Circadian Timing Circuits in Neurospora crassa Cells Share Components and Regulate Distinct Rhythmic Processes. J Biol Rhythms 2016; 21:159-68. [PMID: 16731655 DOI: 10.1177/0748730406288338] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In Neurospora crassa, FRQ, WC-1, and WC-2 proteins comprise the core circadian FRQ-based oscillator that is directly responsive to light and drives daily rhythms in spore development and gene expression. However, physiological and biochemical studies have demonstrated the existence of additional oscillators in the cell that function in the absence of FRQ (collectively termed FRQ-less oscillators [FLOs]). Whether or not these represent temperature-compensated, entrainable circadian oscillators is not known. The authors previously identified an evening-peaking gene, W06H2 (now called clock-controlled gene 16 [ ccg-16]), which is expressed with a robust daily rhythm in cells that lack FRQ protein, suggesting that ccg-16 is regulated by a FLO. In this study, the authors provide evidence that the FLO driving ccg-16 rhythmicity is a circadian oscillator. They find that ccg-16 rhythms are generated by a temperature-responsive, temperature-compensated circadian FLO that, similar to the FRQ-based oscillator, requires functional WC-1 and WC-2 proteins for activity. They also find that FRQ is not essential for rhythmic WC-1 protein levels, raising the possibility that this WCFLO is involved in the generation of WC-1 rhythms. The results are consistent with the presence of 2 circadian oscillators within Neurospora cells, which the authors speculate may interact with each other through the shared WC proteins.
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Affiliation(s)
- Renato M de Paula
- Department of Biology, Center for Research on Biological Clocks, Texas A&M University, College Station, TX 77843, USA
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43
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Abstract
The eukaryotic filamentous fungus Neurospora crassa has proven to be a durable and dependable model system for the analysis of the cellular and molecular bases of circadian rhythms. Pioneering genetic analyses identified clock genes, and beginning with the cloning of frequency ( frq), work over the past 2 decades has revealed the molecular basis of a core circadian clock feedback loop that has illuminated our understanding of circadian oscillators in microbes, plants, and animals. In this transcription/translation-based feedback loop, a heterodimer of the White Collar-1 (WC-1) and WC-2 proteins acts both as the circadian photoreceptor and, in the dark, as a transcription factor that promotes the expression of the frq gene. FRQ dimerizes and feeds back to block the activity of its activators (making a negative feedback loop), as well as feeding forward to promote the synthesis of its activator, WC-1. Phosphorylation of FRQ by several kinases leads to its ubiquitination and turnover, releasing the WC-1/WC-2 dimer to reactivate frq expression and restart the circadian cycle. Light resetting of the clock can be understood through the rapid light induction of frq expression and temperature resetting through the influence of elevated temperaturesin driving higher levels of FRQ. Several FRQ- and WC-independent, noncircadian FRQ-less oscillators (FLOs) have been described, each of which appears to regulate aspects of Neurospora growth or development. Overall, the FRQ/white collar complex feedback loop appears to coordinate the circadian system through its activity to regulate downstream-target clock-controlled genes, either directly or via regulation of driven FLOs.
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Affiliation(s)
- Jay C Dunlap
- Department of Genetics, Dartmouth Medical School, Hannover, NH 03755-3844, USA.
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Abstract
As a biological clock, circadian rhythms evolve to accomplish a stable (robust) entrainment to environmental cycles, of which light is the most obvious. The mechanism of photic entrainment is not known, but two models of entrainment have been proposed based on whether light has a continuous (parametric) or discrete (nonparametric) effect on the circadian pacemaker. A novel sensitivity analysis is developed to study the circadian entrainment in silico based on a limit cycle approach and applied to a model of Drosophila circadian rhythm. The comparative analyses of complete and skeleton photoperiods suggest a trade-off between the contribution of period modulation (parametric effect) and phase shift (nonparametric effect) in Drosophila circadian entrainment. The results also give suggestions for an experimental study to (in)validate the two models of entrainment.
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Affiliation(s)
- Rudiyanto Gunawan
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106-5080, USA
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Solovyov IA, Dobrovol’skaya EV, Moskalev AA. Genetic control of circadian rhythms and aging. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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46
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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Fanelli F, Geisen R, Schmidt-Heydt M, Logrieco A, Mulè G. Light regulation of mycotoxin biosynthesis: new perspectives for food safety. WORLD MYCOTOXIN J 2016. [DOI: 10.3920/wmj2014.1860] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mycotoxins are secondary metabolites produced by toxigenic fungi contaminating foods and feeds in pre-, post-harvest and processing, and represent a great concern worldwide, both for the economic implications and for the health of the consumers. Many environmental conditions are involved in the regulation of mycotoxin biosynthesis. Among these, light represents one of the most important signals for fungi, influencing several physiological responses such as pigmentation, sexual development and asexual conidiation, primary and secondary metabolism, including mycotoxin biosynthesis. In this review we summarise some recent findings on the effect of specific light wavelength and intensity on mycotoxin biosynthesis in the main toxigenic fungal genera. We describe the molecular mechanism underlying light perception and its involvement in the regulation of secondary metabolism, focusing on VeA, global regulator in Aspergillus nidulans, and the White-Collar proteins, key components of light response in Neurospora crassa. Light of specific wavelength and intensity exerts different effects both on growth and on toxin production depending on the fungal genus. In Penicillium spp. red (627 nm) and blue wavelengths (455-470 nm) reduce ochratoxin A (OTA) biosynthesis by modulating the level of expression of the ochratoxin polyketide synthase. Furthermore a mutual regulation between citrinin and OTA production is reported in Penicillium toxigenic species. In Aspergillus spp. the effect of light treatment is strongly dependent on the species and culture conditions. Royal blue wavelength (455 nm) of high intensity (1,700 Lux) is capable of completely inhibit fungal growth and OTA production in Aspergillus stenyii and Penicillum verrucosum. In Fusarium spp. the effect of light exposure is less effective; mycotoxin-producing species, such as Fusarium verticillioides and Fusarium proliferatum, grow better under light conditions, and fumonisin production increased. This review provides a comprehensive picture on light regulation of mycotoxin biosynthesis and discusses possible new applications of this resource in food safety.
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Affiliation(s)
- F. Fanelli
- Institute of Sciences of Food Production, CNR, via Amendola 122/0, 70126 Bari, Italy
| | - R. Geisen
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Haid-und-Neu-Str. 9, 76131 Karlsruhe, Germany
| | - M. Schmidt-Heydt
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Haid-und-Neu-Str. 9, 76131 Karlsruhe, Germany
| | - A.F. Logrieco
- Institute of Sciences of Food Production, CNR, via Amendola 122/0, 70126 Bari, Italy
| | - G. Mulè
- Institute of Sciences of Food Production, CNR, via Amendola 122/0, 70126 Bari, Italy
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Dovzhenok AA, Baek M, Lim S, Hong CI. Mathematical modeling and validation of glucose compensation of the neurospora circadian clock. Biophys J 2016; 108:1830-1839. [PMID: 25863073 DOI: 10.1016/j.bpj.2015.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/05/2014] [Accepted: 01/09/2015] [Indexed: 11/26/2022] Open
Abstract
Autonomous circadian oscillations arise from transcriptional-translational feedback loops of core clock components. The period of a circadian oscillator is relatively insensitive to changes in nutrients (e.g., glucose), which is referred to as "nutrient compensation". Recently, a transcription repressor, CSP-1, was identified as a component of the circadian system in Neurospora crassa. The transcription of csp-1 is under the circadian regulation. Intriguingly, CSP-1 represses the circadian transcription factor, WC-1, forming a negative feedback loop that can influence the core oscillator. This feedback mechanism is suggested to maintain the circadian period in a wide range of glucose concentrations. In this report, we constructed a mathematical model of the Neurospora circadian clock incorporating the above WC-1/CSP-1 feedback loop, and investigated molecular mechanisms of glucose compensation. Our model shows that glucose compensation exists within a narrow range of parameter space where the activation rates of csp-1 and wc-1 are balanced with each other, and simulates loss of glucose compensation in csp-1 mutants. More importantly, we experimentally validated rhythmic oscillations of the wc-1 gene expression and loss of glucose compensation in the wc-1(ov) mutant as predicted in the model. Furthermore, our stochastic simulations demonstrate that the CSP-1-dependent negative feedback loop functions in glucose compensation, but does not enhance the overall robustness of oscillations against molecular noise. Our work highlights predictive modeling of circadian clock machinery and experimental validations employing Neurospora and brings a deeper understanding of molecular mechanisms of glucose compensation.
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Affiliation(s)
- Andrey A Dovzhenok
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Mokryun Baek
- Department of Molecular and Cellular Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Sookkyung Lim
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Christian I Hong
- Department of Molecular and Cellular Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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Alternative Use of DNA Binding Domains by the Neurospora White Collar Complex Dictates Circadian Regulation and Light Responses. Mol Cell Biol 2015; 36:781-93. [PMID: 26711258 DOI: 10.1128/mcb.00841-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/15/2015] [Indexed: 01/09/2023] Open
Abstract
In the Neurospora circadian system, the White Collar complex (WCC) of WC-1 and WC-2 drives transcription of the circadian pacemaker gene frequency (frq), whose gene product, FRQ, as a part of the FRQ-FRH complex (FFC), inhibits its own expression. The WCC is also the principal Neurospora photoreceptor; WCC-mediated light induction of frq resets the clock, and all acute light induction is triggered by WCC binding to promoters of light-induced genes. However, not all acutely light-induced genes are also clock regulated, and conversely, not all clock-regulated direct targets of WCC are light induced; the structural determinants governing the shift from WCC's dark circadian role to its light activation role are poorly described. We report that the DBD region (named for being defective in binding DNA), a basic region in WC-1 proximal to the DNA-binding zinc finger (ZnF) whose function was previously ascribed to nuclear localization, instead plays multiple essential roles assisting in DNA binding and mediating interactions with the FFC. DNA binding for light induction by the WCC requires only WC-2, whereas DNA binding for circadian functions requires WC-2 as well as the ZnF and DBD motif of WC-1. The data suggest a means by which alterations in the tertiary and quaternary structures of the WCC can lead to its distinct functions in the dark and in the light.
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50
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Circadian Control of Global Transcription. BIOMED RESEARCH INTERNATIONAL 2015; 2015:187809. [PMID: 26682214 PMCID: PMC4670846 DOI: 10.1155/2015/187809] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/04/2015] [Indexed: 01/10/2023]
Abstract
Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs). CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions.
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