1
|
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.
Collapse
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
| |
Collapse
|
2
|
Wang B, Dunlap JC. Domains required for the interaction of the central negative element FRQ with its transcriptional activator WCC within the core circadian clock of Neurospora. J Biol Chem 2023; 299:104850. [PMID: 37220856 PMCID: PMC10320511 DOI: 10.1016/j.jbc.2023.104850] [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: 02/25/2023] [Revised: 05/04/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
In the negative feedback loop composing the Neurospora circadian clock, the core element, FREQUENCY (FRQ), binds with FRQ-interacting RNA helicase (FRH) and casein kinase 1 to form the FRQ-FRH complex (FFC) which represses its own expression by interacting with and promoting phosphorylation of its transcriptional activators White Collar-1 (WC-1) and WC-2 (together forming the White Collar complex, WCC). Physical interaction between FFC and WCC is a prerequisite for the repressive phosphorylations, and although the motif on WCC needed for this interaction is known, the reciprocal recognition motif(s) on FRQ remains poorly defined. To address this, we assessed FFC-WCC in a series of frq segmental-deletion mutants, confirming that multiple dispersed regions on FRQ are necessary for its interaction with WCC. Biochemical analysis shows that interaction between FFC and WCC but not within FFC or WCC can be disrupted by high salt, suggesting that electrostatic forces drive the association of the two complexes. As a basic sequence on WC-1 was previously identified as a key motif for WCC-FFC assembly, our mutagenetic analysis targeted negatively charged residues of FRQ, leading to identification of three Asp/Glu clusters in FRQ that are indispensable for FFC-WCC formation. Surprisingly, in several frq Asp/Glu-to-Ala mutants that vastly diminish FFC-WCC interaction, the core clock still oscillates robustly with an essentially wildtype period, indicating that the interaction between the positive and negative elements in the feedback loop is required for the operation of the circadian clock but is not a determinant of the period length.
Collapse
Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| |
Collapse
|
3
|
Wang B, Zhou X, Kettenbach AN, Mitchell HD, Markillie LM, Loros JJ, Dunlap JC. A crucial role for dynamic expression of components encoding the negative arm of the circadian clock. Nat Commun 2023; 14:3371. [PMID: 37291101 PMCID: PMC10250352 DOI: 10.1038/s41467-023-38817-7] [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: 08/10/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency (frq). FRQ interacts with FRH (FRQ-interacting RNA helicase) and CKI, forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8, that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone h2a.z, and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.
Collapse
Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
| | - Xiaoying Zhou
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Hugh D Mitchell
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Lye Meng Markillie
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jennifer J Loros
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- 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.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Wang B, Dunlap JC. Domains Required for FRQ-WCC Interaction within the Core Circadian Clock of Neurospora. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530043. [PMID: 36865291 PMCID: PMC9980274 DOI: 10.1101/2023.02.25.530043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In the negative feedback loop composing the Neurospora circadian clock, the core element, FREQUENCY (FRQ) binds with FRH (FRQ-interacting RNA helicase) and Casein Kinase 1 (CK1) to form the FRQ-FRH complex (FFC) which represses its own expression by interacting with and promoting phosphorylation of its transcriptional activators White Collar-1 (WC-1) and WC-2 (together forming the White Collar Complex, WCC). Physical interaction between FFC and WCC is a prerequisite for the repressive phosphorylations, and although the motif on WCC needed for this interaction is known, the reciprocal recognition motif(s) on FRQ remains poorly defined. To address this, FFC-WCC was assessed in a series of frq segmental-deletion mutants, confirming that multiple dispersed regions on FRQ are necessary for its interaction with WCC. Biochemical analysis shows that interaction between FFC and WCC but not within FFC or WCC can be disrupted by high salt, suggesting that electrostatic forces drive the association of the two complexes. As a basic sequence on WC-1 was previously identified as a key motif for WCC-FFC assembly, our mutagenetic analysis targeted negatively charged residues of FRQ leading to identification of three Asp/Glu clusters in FRQ that are indispensable for FFC-WCC formation. Surprisingly, in several frq Asp/Glu-to-Ala mutants that vastly diminish FFC-WCC interaction, the core clock still oscillates robustly with an essentially WT period, indicating that the binding strength between the positive and negative elements in the feedback loop is required for the clock but is not a determinant of the period length.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Kelliher CM, Stevenson EL, Loros JJ, Dunlap JC. Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability. PLoS Biol 2023; 21:e3001961. [PMID: 36603054 PMCID: PMC9848017 DOI: 10.1371/journal.pbio.3001961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 01/18/2023] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator's period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured human cells, we selected top hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian orthologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down the mammalian orthologs of the Neurospora compensation-associated genes CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.
Collapse
Affiliation(s)
- Christina M. Kelliher
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Elizabeth-Lauren Stevenson
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jennifer J. Loros
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jay C. Dunlap
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| |
Collapse
|
8
|
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.
Collapse
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)
| |
Collapse
|
9
|
Peng H, Zhang YL, Ying SH, Feng MG. The Essential and the Nonessential Roles of Four Clock Elements in the Circadian Rhythm of Metarhizium robertsii. J Fungi (Basel) 2022; 8:jof8060558. [PMID: 35736041 PMCID: PMC9224670 DOI: 10.3390/jof8060558] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
FRQ (frequency protein), FRH (FRQ-interacting RNA helicase), and WC1 and WC2 (white collar proteins) are major clock elements that govern the circadian rhythm in Neurospora crassa. However, deletion of frh is lethal for the viability of N. crassa, making it elusive whether FRH is essential or nonessential for the circadian rhythm. This needs clarification in a fungus where frh deletion is not lethal. Here, the nuclear FRH ortholog proved nonessential for the circadian rhythm of Metarhizium robertsii. The nucleocytoplasmic shuttling of M. robertsii FRQ, WC1, and WC2 orthologs was light-dependent. Yeast two-hybrid assay validated interactions of FRQ with FRH and WC1 instead of FRH with WC1 and WC2 or FRQ with WC2. The circadian rhythm well, shown as conidiation rings of tint and dark in 15 d-old plate cultures grown at 25 °C in a light/dark cycle of 12:12, was abolished in the absence of frq or wc1, partially disturbed in the absence of wc2, but unaffected in the absence of frh. These results indicate a requirement of either FRQ or WC1 instead of FRH for the fungal circadian rhythm. Further analyses of frq and frh mutants revealed the dispensable and the limited roles of FRQ and FRH in the insect-pathogenic lifecycle of M. robertsii, respectively.
Collapse
|
10
|
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.
Collapse
|
11
|
Molecular Regulation of Circadian Chromatin. J Mol Biol 2020; 432:3466-3482. [PMID: 31954735 DOI: 10.1016/j.jmb.2020.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/13/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
Circadian rhythms are generated by transcriptional negative feedback loops and require histone modifications and chromatin remodeling to ensure appropriate timing and amplitude of clock gene expression. Circadian modifications to histones are important for transcriptional initiation and feedback inhibition serving as signaling platform for chromatin-remodeling enzymes. Current models indicate circadian-regulated facultative heterochromatin (CRFH) is a conserved mechanism at clock genes in Neurospora, Drosophila, and mice. CRFH consists of antiphasic rhythms in activating and repressive modifications generating chromatin states that cycle between transcriptionally permissive and nonpermissive. There are rhythms in histone H3 lysine 9 and 27 acetylation (H3K9ac and H3K27ac) and histone H3 lysine 4 methylation (H3K4me) during activation; while deacetylation, histone H3 lysine 9 methylation (H3K9me) and heterochromatin protein 1 (HP1) are hallmarks of repression. ATP-dependent chromatin-remodeling enzymes control accessibility, nucleosome positioning/occupancy, and nuclear organization. In Neurospora, the rhythm in facultative heterochromatin is mediated by the frequency (frq) natural antisense transcript (NAT) qrf. While in mammals, histone deacetylases (HDACs), histone H3 lysine 9 methyltransferase (KMT1/SUV39), and components of nucleosome remodeling and deacetylase (NuRD) are part of the nuclear PERIOD complex (PER complex). Genomics efforts have found relationships among rhythmic chromatin modifications at clock-controlled genes (ccg) revealing circadian control of genome-wide chromatin states. There are also circadian clock-regulated lncRNAs with an emerging function that includes assisting in chromatin dynamics. In this review, we explore the connections between circadian clock, chromatin remodeling, lncRNAs, and CRFH and how these impact rhythmicity, amplitude, period, and phase of circadian clock genes.
Collapse
|
12
|
Singh SN, Malik M, Singh RKB. Towards the revival of oscillation from complete cessation in stochastic systems for application in molecular biology. Bioinformation 2020; 16:274-282. [PMID: 32308270 PMCID: PMC7147491 DOI: 10.6026/97320630016274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/05/2020] [Accepted: 03/17/2020] [Indexed: 11/23/2022] Open
Abstract
Delay and noise are inevitable in complex systems that are common in biochemical networks. The system is often disturbed at various states irrespective of the size (small or large) of delay and noise. Therefore, it is of interest to describe the significance of delay and noise in stochastic Willamowski-Rossler chemical oscillator model using a delay stochastic (having random probability distribution) simulation algorithm. Oscillating dynamics moves to stable fixed point when delay at a fixed magnitude of noise drives the system from oscillating state to stochastic amplitude death state (complete cessation). However, the amplitude death state is induced to a revived oscillating state in stochastic system (which is far from equilibrium state) for noise with a fixed value of delay. Thus, significantly large and small noise induces the dynamics of the system to amplitude death state. Hence, we describe the interplay of delay and noise in stochastic systems for the proper and efficient functioning of the complex system that are frequent in biological networks.
Collapse
Affiliation(s)
- Shakti Nath Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Md.Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - RK Brojen Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
13
|
Tong SM, Wang DY, Cai Q, Ying SH, Feng MG. Opposite Nuclear Dynamics of Two FRH-Dominated Frequency Proteins Orchestrate Non-Rhythmic Conidiation in Beauveria bassiana. Cells 2020; 9:cells9030626. [PMID: 32151014 PMCID: PMC7140403 DOI: 10.3390/cells9030626] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022] Open
Abstract
Non-rhythmic conidiation favors large-scale production of conidia serving as active ingredients of fungal insecticides, but its regulatory mechanism is unknown. Here, we report that two FREQUENCY (FRQ) proteins (Frq1/2) governed by a unique FRQ-interacting RNA helicase (FRH) orchestrate this valuable trait in Beauveria bassiana, an asexual insect-pathogenic fungus. Frq1 (964 aa) and Frq2 (583 aa) exhibited opposite expression dynamics (rhythms) in nucleus and steadily high expression levels in cytoplasm under light or in darkness no matter whether one of them was present or absent. Such opposite nuclear dynamics presented a total FRQ (pooled Frq1/2) level sufficient to persistently activate central developmental pathway in daytime and nighttime and supports continuous (non-rhythmic) conidiation for rapid maximization of conidial production in a fashion independent of photoperiod change. Importantly, both nuclear dynamics and cytoplasmic stability of Frq1 and Frq2 were abolished in the absence of the FRH-coding gene nonessential for the fungal viability, highlighting an indispensability of FRH for the behaviors of Frq1 and Frq2 in both nucleus and cytoplasm. These findings uncover a novel circadian system more complicated than the well-known Neurospora model that controls rhythmic conidiation, and provide a novel insight into molecular control of non-rhythmic conidiation in B. bassiana.
Collapse
Affiliation(s)
- Sen-Miao Tong
- College of Agricultural and Food Science, Zhejiang A&F University, Lin’an 311300, Zhejiang, China
- Correspondence: (S.M.T.); (M.G.F.)
| | - Ding-Yi Wang
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Qing Cai
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Sheng-Hua Ying
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Correspondence: (S.M.T.); (M.G.F.)
| |
Collapse
|
14
|
FRQ-CK1 interaction determines the period of circadian rhythms in Neurospora. Nat Commun 2019; 10:4352. [PMID: 31554810 PMCID: PMC6761100 DOI: 10.1038/s41467-019-12239-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/28/2019] [Indexed: 01/25/2023] Open
Abstract
Circadian clock mechanisms have been extensively investigated but the main rate-limiting step that determines circadian period remains unclear. Formation of a stable complex between clock proteins and CK1 is a conserved feature in eukaryotic circadian mechanisms. Here we show that the FRQ-CK1 interaction, but not FRQ stability, correlates with circadian period in Neurospora circadian clock mutants. Mutations that specifically affect the FRQ-CK1 interaction lead to severe alterations in circadian period. The FRQ-CK1 interaction has two roles in the circadian negative feedback loop. First, it determines the FRQ phosphorylation profile, which regulates FRQ stability and also feeds back to either promote or reduce the interaction itself. Second, it determines the efficiency of circadian negative feedback process by mediating FRQ-dependent WC phosphorylation. Our conclusions are further supported by mathematical modeling and in silico experiments. Together, these results suggest that the FRQ-CK1 interaction is a major rate-limiting step in circadian period determination. Circadian clocks control daily rhythms of molecular and physiological activities. Here, the authors show that the interaction between proteins FRQ and CK1, rather than FRQ stability, is a major rate-limiting step in circadian period determination in the model fungus Neurospora.
Collapse
|
15
|
Circadian clock regulation of the glycogen synthase ( gsn) gene by WCC is critical for rhythmic glycogen metabolism in Neurospora crassa. Proc Natl Acad Sci U S A 2019; 116:10435-10440. [PMID: 31048503 PMCID: PMC6534987 DOI: 10.1073/pnas.1815360116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Circadian rhythms enable organisms to anticipate daily environmental cycles and control the timing of numerous biological processes, including metabolism, to optimize the health and survival of organisms. Glycogen metabolism is a conserved glucose homeostatic process; however, the molecular mechanisms linking the circadian clock and glycogen metabolism remain largely unknown. In this report, we demonstrate that circadian clock-dependent transcriptional regulation of glycogen synthase, gsn, regulates circadian oscillations of GSN protein and glycogen accumulation in the model filamentous fungus, Neurospora crassa. Circadian clocks generate rhythms in cellular functions, including metabolism, to align biological processes with the 24-hour environment. Disruption of this alignment by shift work alters glucose homeostasis. Glucose homeostasis depends on signaling and allosteric control; however, the molecular mechanisms linking the clock to glucose homeostasis remain largely unknown. We investigated the molecular links between the clock and glycogen metabolism, a conserved glucose homeostatic process, in Neurospora crassa. We find that glycogen synthase (gsn) mRNA, glycogen phosphorylase (gpn) mRNA, and glycogen levels, accumulate with a daily rhythm controlled by the circadian clock. Because the synthase and phosphorylase are critical to homeostasis, their roles in generating glycogen rhythms were investigated. We demonstrate that while gsn was necessary for glycogen production, constitutive gsn expression resulted in high and arrhythmic glycogen levels, and deletion of gpn abolished gsn mRNA rhythms and rhythmic glycogen accumulation. Furthermore, we show that gsn promoter activity is rhythmic and is directly controlled by core clock component white collar complex (WCC). We also discovered that WCC-regulated transcription factors, VOS-1 and CSP-1, modulate the phase and amplitude of rhythmic gsn mRNA, and these changes are similarly reflected in glycogen oscillations. Together, these data indicate the importance of clock-regulated gsn transcription over signaling or allosteric control of glycogen rhythms, a mechanism that is potentially conserved in mammals and critical to metabolic homeostasis.
Collapse
|
16
|
The Phospho-Code Determining Circadian Feedback Loop Closure and Output in Neurospora. Mol Cell 2019; 74:771-784.e3. [PMID: 30954403 DOI: 10.1016/j.molcel.2019.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/07/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
In the negative feedback loop driving fungal and animal circadian oscillators, negative elements (FREQUENCY [FRQ], PERIODS [PERs], and CRYPTOCHROMES [CRYs]) are understood to inhibit their own expression, in part by promoting the phosphorylation of their heterodimeric transcriptional activators (e.g., White Collar-1 [WC-1]-WC-2 [White Collar complex; WCC] and BMAL1/Circadian Locomotor Output Cycles Kaput [CLOCK]). However, correlations between heterodimer activity and phosphorylation are weak, contradictions exist, and mechanistic details are almost wholly lacking. We report mapping of 80 phosphosites on WC-1 and 15 on WC-2 and elucidation of the time-of-day-specific code, requiring both a group of phosphoevents on WC-1 and two distinct clusters on WC-2, that governs circadian repression, leading to feedback loop closure. Combinatorial control via phosphorylation also governs rhythmic WCC binding to the promoters of clock-controlled genes mediating the essential first step in circadian output, a group encoding both transcription factors and signaling proteins. These data provide a basic mechanistic understanding for fundamental events underlying circadian negative feedback and output, key aspects of circadian biology.
Collapse
|
17
|
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]
|
18
|
Kaity B, Sarkar R, Chakrabarti B, Mitra MK. Reprogramming, oscillations and transdifferentiation in epigenetic landscapes. Sci Rep 2018; 8:7358. [PMID: 29743499 PMCID: PMC5943272 DOI: 10.1038/s41598-018-25556-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/19/2018] [Indexed: 11/21/2022] Open
Abstract
Waddington’s epigenetic landscape provides a phenomenological understanding of the cell differentiation pathways from the pluripotent to mature lineage-committed cell lines. In light of recent successes in the reverse programming process there has been significant interest in quantifying the underlying landscape picture through the mathematics of gene regulatory networks. We investigate the role of time delays arising from multi-step chemical reactions and epigenetic rearrangement on the cell differentiation landscape for a realistic two-gene regulatory network, consisting of self-promoting and mutually inhibiting genes. Our work provides the first theoretical basis of the transdifferentiation process in the presence of delays, where one differentiated cell type can transition to another directly without passing through the undifferentiated state. Additionally, the interplay of time-delayed feedback and a time dependent chemical drive leads to long-lived oscillatory states in appropriate parameter regimes. This work emphasizes the important role played by time-delayed feedback loops in gene regulatory circuits and provides a framework for the characterization of epigenetic landscapes.
Collapse
Affiliation(s)
- Bivash Kaity
- IIT Bombay, Department of Physics, Mumbai, 400076, India
| | - Ratan Sarkar
- Indian Institute of Science, Centre for High Energy Physics, Bangalore, 560012, India
| | | | - Mithun K Mitra
- IIT Bombay, Department of Physics, Mumbai, 400076, India.
| |
Collapse
|
19
|
Liversage J, Coetzee MP, Bluhm BH, Berger DK, Crampton BG. LOVe across kingdoms: Blue light perception vital for growth and development in plant–fungal interactions. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Liu X, Dang Y, Matsu-Ura T, He Y, He Q, Hong CI, Liu Y. DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition. Mol Cell 2017. [PMID: 28648778 DOI: 10.1016/j.molcel.2017.05.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle. Here, we show that DNA replication is required for circadian clock function in Neurospora. Genetic and pharmacological inhibition of DNA replication abolished both overt and molecular rhythmicities by repressing frequency (frq) gene transcription. DNA replication is essential for the rhythmic changes of nucleosome composition at the frq promoter. The FACT complex, known to be involved in histone disassembly/reassembly, is required for clock function and is recruited to the frq promoter in a replication-dependent manner to promote replacement of histone H2A.Z by H2A. Finally, deletion of H2A.Z uncoupled the dependence of the circadian clock on DNA replication. Together, these results establish circadian clock and cell cycle as interdependent coupled oscillators and identify DNA replication as a critical process in the circadian mechanism.
Collapse
Affiliation(s)
- Xiao Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Toru Matsu-Ura
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yubo He
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA; Department of Biochemistry and Cell Biology, McMurtry College, Rice University, Houston, TX 77005, USA
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Christian I Hong
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.
| |
Collapse
|
22
|
Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion. G3 (BETHESDA, MD.) 2017; 7:129-142. [PMID: 27856696 PMCID: PMC5217103 DOI: 10.1534/g3.116.034298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.
Collapse
Affiliation(s)
- Rigzin Dekhang
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Teresa M Lamb
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | | | - Erin L Bredeweg
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Oneida Ibarra
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jillian M Emerson
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | | | | | - Elham Azizi
- Bioinformatics Program, Boston University, Massachusetts 02215
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - James E Galagan
- Bioinformatics Program, Boston University, Massachusetts 02215
- National Emerging Infectious Diseases Laboratories, Boston University, Massachusetts 02118
- Department of Microbiology, Boston University, Massachusetts 02215
- Department of Biomedical Engineering, Boston University, Massachusetts 02215
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | | |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Renato M de Paula
- Department of Biology, Center for Research on Biological Clocks, Texas A&M University, College Station, TX 77843, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Conrad KS, Hurley JM, Widom J, Ringelberg CS, Loros JJ, Dunlap JC, Crane BR. Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock. EMBO J 2016; 35:1707-19. [PMID: 27340124 PMCID: PMC4969578 DOI: 10.15252/embj.201694327] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/23/2016] [Indexed: 11/09/2022] Open
Abstract
In the Neurospora crassa circadian clock, a protein complex of frequency (FRQ), casein kinase 1a (CK1a), and the FRQ-interacting RNA Helicase (FRH) rhythmically represses gene expression by the white-collar complex (WCC). FRH crystal structures in several conformations and bound to ADP/RNA reveal differences between FRH and the yeast homolog Mtr4 that clarify the distinct role of FRH in the clock. The FRQ-interacting region at the FRH N-terminus has variable structure in the absence of FRQ A known mutation that disrupts circadian rhythms (R806H) resides in a positively charged surface of the KOW domain, far removed from the helicase core. We show that changes to other similarly located residues modulate interactions with the WCC and FRQ A V142G substitution near the N-terminus also alters FRQ and WCC binding to FRH, but produces an unusual short clock period. These data support the assertion that FRH helicase activity does not play an essential role in the clock, but rather FRH acts to mediate contacts among FRQ, CK1a and the WCC through interactions involving its N-terminus and KOW module.
Collapse
Affiliation(s)
- Karen S Conrad
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Joanne Widom
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Jennifer J Loros
- Department of Biochemistry, Geisel School of Medicine, Hanover, NH, USA
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine, Hanover, NH, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Fuller K, Dunlap J, Loros J. Fungal Light Sensing at the Bench and Beyond. ADVANCES IN GENETICS 2016; 96:1-51. [DOI: 10.1016/bs.adgen.2016.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
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.
Collapse
|
29
|
Role for Protein Kinase A in the Neurospora Circadian Clock by Regulating White Collar-Independent frequency Transcription through Phosphorylation of RCM-1. Mol Cell Biol 2015; 35:2088-102. [PMID: 25848091 DOI: 10.1128/mcb.00709-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 03/30/2015] [Indexed: 01/24/2023] Open
Abstract
Rhythmic activation and repression of clock gene expression is essential for the eukaryotic circadian clock functions. In the Neurospora circadian oscillator, the transcription of the frequency (frq) gene is periodically activated by the White Collar (WC) complex and suppressed by the FRQ-FRH complex. We previously showed that there is WC-independent frq transcription and its repression is required for circadian gene expression. How WC-independent frq transcription is regulated is not known. We show here that elevated protein kinase A (PKA) activity results in WC-independent frq transcription and the loss of clock function. We identified RCM-1 as the protein partner of RCO-1 and an essential component of the clock through its role in suppressing WC-independent frq transcription. RCM-1 is a phosphoprotein and is a substrate of PKA in vivo and in vitro. Mutation of the PKA-dependent phosphorylation sites on RCM-1 results in WC-independent transcription of frq and impaired clock function. Furthermore, we showed that RCM-1 is associated with the chromatin at the frq locus, a process that is inhibited by PKA. Together, our results demonstrate that PKA regulates frq transcription by inhibiting RCM-1 activity through RCM-1 phosphorylation.
Collapse
|
30
|
The frequency natural antisense transcript first promotes, then represses, frequency gene expression via facultative heterochromatin. Proc Natl Acad Sci U S A 2015; 112:4357-62. [PMID: 25831497 DOI: 10.1073/pnas.1406130112] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock is controlled by a network of interconnected feedback loops that require histone modifications and chromatin remodeling. Long noncoding natural antisense transcripts (NATs) originate from Period in mammals and frequency (frq) in Neurospora. To understand the role of NATs in the clock, we put the frq antisense transcript qrf (frq spelled backwards) under the control of an inducible promoter. Replacing the endogenous qrf promoter altered heterochromatin formation and DNA methylation at frq. In addition, constitutive, low-level induction of qrf caused a dramatic effect on the endogenous rhythm and elevated circadian output. Surprisingly, even though qrf is needed for heterochromatic silencing, induction of qrf initially promoted frq gene expression by creating a more permissible local chromatin environment. The observation that antisense expression can initially promote sense gene expression before silencing via heterochromatin formation at convergent loci is also found when a NAT to hygromycin resistance gene is driven off the endogenous vivid (vvd) promoter in the Δvvd strain. Facultative heterochromatin silencing at frq functions in a parallel pathway to previously characterized VVD-dependent silencing and is needed to establish the appropriate circadian phase. Thus, repression via dicer-independent siRNA-mediated facultative heterochromatin is largely independent of, and occurs alongside, other feedback processes.
Collapse
|
31
|
Abstract
![]()
Circadian clocks are self-sustaining
timekeepers found in almost
all organisms on earth. The filamentous fungus Neurospora
crassa is a preeminent model for eukaryotic circadian clocks.
Investigations of the Neurospora circadian clock
system have led to elucidation of circadian clock regulatory mechanisms
that are common to all eukaryotes. In this work, we will focus on
the Neurospora circadian oscillator mechanism with
an emphasis on the regulation of the core clock component FREQUENCY.
Collapse
Affiliation(s)
- Joonseok Cha
- Department of Physiology, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390-9040, United States
| | | | | |
Collapse
|
32
|
The histone H3 lysine 9 methyltransferase DIM-5 modifies chromatin at frequency and represses light-activated gene expression. G3-GENES GENOMES GENETICS 2014; 5:93-101. [PMID: 25429045 PMCID: PMC4291474 DOI: 10.1534/g3.114.015446] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The transcriptional program controlling the circadian rhythm requires coordinated regulation of chromatin. Characterization of the chromodomain helicase DNA-binding enzyme CHD1 revealed DNA methylation in the promoter of the central clock gene frequency (frq) in Neurospora crassa. In this report, we show that the DNA methylation at frq is not only dependent on the DNA methyltransferase DIM-2 but also on the H3K9 methyltransferase DIM-5 and HP1. Histone H3 lysine 9 trimethylation (H3K9me3) occurs at frq and is most prominent 30 min after light-activated expression. Strains lacking dim-5 have an increase in light-induced transcription, and more White Collar-2 is found associated with the frq promoter. Consistent with the notion that DNA methylation assists in establishing the proper circadian phase, loss of H3K9 methylation results in a phase advance suggesting it delays the onset of frq expression. The dim-5 deletion strain displays an increase in circadian-regulated conidia formation on race tubes and there is a synthetic genetic interaction between dim-5 and ras-1bd. These results indicate DIM-5 has a regulatory role in muting circadian output. Overall, the data support a model where facultative heterochromatic at frq serves to establish the appropriate phase, mute the light response, and repress circadian output.
Collapse
|
33
|
Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc Natl Acad Sci U S A 2014; 111:16995-7002. [PMID: 25362047 DOI: 10.1073/pnas.1418963111] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Neurospora crassa has been for decades a principal model for filamentous fungal genetics and physiology as well as for understanding the mechanism of circadian clocks. Eukaryotic fungal and animal clocks comprise transcription-translation-based feedback loops that control rhythmic transcription of a substantial fraction of these transcriptomes, yielding the changes in protein abundance that mediate circadian regulation of physiology and metabolism: Understanding circadian control of gene expression is key to understanding eukaryotic, including fungal, physiology. Indeed, the isolation of clock-controlled genes (ccgs) was pioneered in Neurospora where circadian output begins with binding of the core circadian transcription factor WCC to a subset of ccg promoters, including those of many transcription factors. High temporal resolution (2-h) sampling over 48 h using RNA sequencing (RNA-Seq) identified circadianly expressed genes in Neurospora, revealing that from ∼10% to as much 40% of the transcriptome can be expressed under circadian control. Functional classifications of these genes revealed strong enrichment in pathways involving metabolism, protein synthesis, and stress responses; in broad terms, daytime metabolic potential favors catabolism, energy production, and precursor assembly, whereas night activities favor biosynthesis of cellular components and growth. Discriminative regular expression motif elicitation (DREME) identified key promoter motifs highly correlated with the temporal regulation of ccgs. Correlations between ccg abundance from RNA-Seq, the degree of ccg-promoter activation as reported by ccg-promoter-luciferase fusions, and binding of WCC as measured by ChIP-Seq, are not strong. Therefore, although circadian activation is critical to ccg rhythmicity, posttranscriptional regulation plays a major role in determining rhythmicity at the mRNA level.
Collapse
|
34
|
Abstract
The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 hr in the dark and then exposed to light for 0 (control) 15, 60, 120, and 240 min. More than three-quarters of all defined protein coding genes (79%) were expressed in these cells. The increased sensitivity of RNA-seq compared with previous microarray studies revealed that the RNA levels for 31% of expressed genes were affected two-fold or more by exposure to light. Additionally, a large class of mRNAs, enriched for transcripts specifying products involved in rRNA metabolism, showed decreased expression in response to light, indicating a heretofore undocumented effect of light on this pathway. Based on measured changes in mRNA levels, light generally increases cellular metabolism and at the same time causes significant oxidative stress to the organism. To deal with this stress, protective photopigments are made, antioxidants are produced, and genes involved in ribosome biogenesis are transiently repressed.
Collapse
|
35
|
Eliaš J, Clairambault J. Reaction-diffusion systems for spatio-temporal intracellular protein networks: A beginner's guide with two examples. Comput Struct Biotechnol J 2014; 10:12-22. [PMID: 25210594 PMCID: PMC4151873 DOI: 10.1016/j.csbj.2014.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Spatio-temporal dynamics of a variety of proteins is, among other things, regulated by post-translational modifications of these proteins. Such modifications can thus influence stability and biochemical activities of the proteins, activity and stability of their upstream targets within specific signalling pathways. Commonly used mathematical tools for such protein–protein (and/or protein-mRNA) interactions in single cells, namely, Michaelis–Menten and Hill kinetics, yielding a system of ordinary differential equations, are extended here into (non-linear) partial differential equations by taking into account a more realistic spatial representation of the environment where these reactions occur. In the modelling framework under consideration, all interactions occur in a cell divided into two compartments, the nucleus and the cytoplasm, connected by the semipermeable nuclear membrane and bounded by the impermeable cell membrane. Passive transport mechanism, modelled by the so-called Kedem–Katchalsky boundary conditions, is used here to represent migration of species throughout the nuclear membrane. Nonlinear systems of partial differential equations are solved by the semi-implicit Rothe method. Examples of two spatial oscillators are shown. Namely, these are the circadian rhythm for concentration of the FRQ protein in Neurospora crassa and oscillatory dynamics observed in the activation and regulation of the p53 protein following DNA damage in mammalian cells.
Collapse
Affiliation(s)
- Ján Eliaš
- Université Pierre et Marie Curie Paris 06, Sorbonne Universités, Laboratoire Jacques-Louis Lions, boîte courrier 187, F75253 Cedex 05, Paris, France
| | - Jean Clairambault
- Université Pierre et Marie Curie Paris 06, Sorbonne Universités, Laboratoire Jacques-Louis Lions, boîte courrier 187, F75253 Cedex 05, Paris, France
| |
Collapse
|
36
|
Abstract
The cell cycle and the circadian clock communicate with each other, resulting in circadian-gated cell division cycles. Alterations in this network may lead to diseases such as cancer. Therefore, it is critical to identify molecular components that connect these two oscillators. However, molecular mechanisms between the clock and the cell cycle remain largely unknown. A model filamentous fungus, Neurospora crassa, is a multinucleate system used to elucidate molecular mechanisms of circadian rhythms, but not used to investigate the molecular coupling between these two oscillators. In this report, we show that a conserved coupling between the circadian clock and the cell cycle exists via serine/threonine protein kinase-29 (STK-29), the Neurospora homolog of mammalian WEE1 kinase. Based on this finding, we established a mathematical model that predicts circadian oscillations of cell cycle components and circadian clock-dependent synchronized nuclear divisions. We experimentally demonstrate that G1 and G2 cyclins, CLN-1 and CLB-1, respectively, oscillate in a circadian manner with bioluminescence reporters. The oscillations of clb-1 and stk-29 gene expression are abolished in a circadian arrhythmic frq(ko) mutant. Additionally, we show the light-induced phase shifts of a core circadian component, frq, as well as the gene expression of the cell cycle components clb-1 and stk-29, which may alter the timing of divisions. We then used a histone hH1-GFP reporter to observe nuclear divisions over time, and show that a large number of nuclear divisions occur in the evening. Our findings demonstrate the circadian clock-dependent molecular dynamics of cell cycle components that result in synchronized nuclear divisions in Neurospora.
Collapse
|
37
|
Hurley JM, Larrondo LF, Loros JJ, Dunlap JC. Conserved RNA helicase FRH acts nonenzymatically to support the intrinsically disordered neurospora clock protein FRQ. Mol Cell 2013; 52:832-43. [PMID: 24316221 DOI: 10.1016/j.molcel.2013.11.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 10/08/2013] [Accepted: 10/31/2013] [Indexed: 11/24/2022]
Abstract
Protein conformation dictates a great deal of protein function. A class of naturally unstructured proteins, termed intrinsically disordered proteins (IDPs), demonstrates that flexibility in structure can be as important mechanistically as rigid structure. At the core of the circadian transcription/translation feedback loop in Neurospora crassa is the protein FREQUENCY (FRQ), shown here shown to share many characteristics of IDPs. FRQ in turn binds to FREQUENCY-Interacting RNA Helicase (FRH), whose clock function has been assumed to relate to its predicted helicase function. However, mutational analyses reveal that the helicase function of FRH is not essential for the clock, and a region of FRH distinct from the helicase region is essential for stabilizing FRQ against rapid degradation via a pathway distinct from its typical ubiquitin-mediated turnover. These data lead to the hypothesis that FRQ is an IDP and that FRH acts nonenzymatically, stabilizing FRQ to enable proper clock circuitry/function.
Collapse
Affiliation(s)
- Jennifer M Hurley
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Luis F Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Jennifer J Loros
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| |
Collapse
|
38
|
Regulation of transcription by light in Neurospora crassa: A model for fungal photobiology? FUNGAL BIOL REV 2013. [DOI: 10.1016/j.fbr.2013.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
39
|
Simulation of E. coli gene regulation including overlapping cell cycles, growth, division, time delays and noise. PLoS One 2013; 8:e62380. [PMID: 23638057 PMCID: PMC3637171 DOI: 10.1371/journal.pone.0062380] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 03/22/2013] [Indexed: 11/19/2022] Open
Abstract
Due to the complexity of biological systems, simulation of biological networks is necessary but sometimes complicated. The classic stochastic simulation algorithm (SSA) by Gillespie and its modified versions are widely used to simulate the stochastic dynamics of biochemical reaction systems. However, it has remained a challenge to implement accurate and efficient simulation algorithms for general reaction schemes in growing cells. Here, we present a modeling and simulation tool, called ‘GeneCircuits’, which is specifically developed to simulate gene-regulation in exponentially growing bacterial cells (such as E. coli) with overlapping cell cycles. Our tool integrates three specific features of these cells that are not generally included in SSA tools: 1) the time delay between the regulation and synthesis of proteins that is due to transcription and translation processes; 2) cell cycle-dependent periodic changes of gene dosage; and 3) variations in the propensities of chemical reactions that have time-dependent reaction rates as a consequence of volume expansion and cell division. We give three biologically relevant examples to illustrate the use of our simulation tool in quantitative studies of systems biology and synthetic biology.
Collapse
|
40
|
Raduwan H, Isola AL, Belden WJ. Methylation of histone H3 on lysine 4 by the lysine methyltransferase SET1 protein is needed for normal clock gene expression. J Biol Chem 2013; 288:8380-8390. [PMID: 23319591 PMCID: PMC3605655 DOI: 10.1074/jbc.m112.359935] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The circadian oscillator controls time-of-day gene expression by a network of interconnected feedback loops and is reset by light. The requisite for chromatin regulation in eukaryotic transcription necessitates temporal regulation of histone-modifying and chromatin-remodeling enzymes for proper clock function. CHD1 is known to bind H3K4me3 in mammalian cells, and Neurospora CHD1 is required for proper regulation of the frequency (frq) gene. Based on this, we examined a strain lacking SET1 to determine the role of H3K4 methylation in clock- and light-mediated frq regulation. Expression of frq was altered in strains lacking set1 under both circadian- and light-regulated gene expression. There is a delay in the phasing of H3K4me3 relative to the peak in frq expression. White Collar 2 (WC-2) association with the frq promoter persists longer in Δset1, suggesting a more permissible chromatin state. Surprisingly, SET1 is required for DNA methylation in the frq promoter, indicating a dependence on H3K4me for DNA methylation. The data support a model where SET1 is needed for proper regulation by modulating chromatin at frq.
Collapse
Affiliation(s)
- Hamidah Raduwan
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Allison L Isola
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - William J Belden
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901.
| |
Collapse
|
41
|
Jiang H, Hou Z. Delay induced bifurcation of dominant transition pathways. CHAOS (WOODBURY, N.Y.) 2012; 22:033141. [PMID: 23020480 DOI: 10.1063/1.4749795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We investigate delay effects on dominant transition pathways (DTP) between metastable states of stochastic systems. A modified version of the Maier-Stein model with linear delayed feedback is considered as an example. By a stability analysis of the "on-axis" DTP in trajectory space, we find that a bifurcation of DTPs will be induced when time delay τ is large enough. This finding is soon verified by numerically derived DTPs which are calculated by employing a recently developed minimum action method extended to delayed stochastic systems. Further simulation shows that the delay-induced bifurcation of DTPs also results in a nontrivial dependence of the transition rate constant on the delay time. Finally, the bifurcation diagram is given on the τ-β plane, where β measures the non-conservation of the original Maier-Stein model.
Collapse
Affiliation(s)
- Huijun Jiang
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | | |
Collapse
|
42
|
ENVOY is a major determinant in regulation of sexual development in Hypocrea jecorina (Trichoderma reesei). EUKARYOTIC CELL 2012; 11:885-95. [PMID: 22581525 DOI: 10.1128/ec.05321-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Light is one crucial environmental signal which can determine whether a fungus reproduces asexually or initiates sexual development. Mating in the ascomycete Hypocrea jecorina (anamorph Trichoderma reesei) occurs preferentially in light. We therefore investigated the relevance of the light response machinery for sexual development in H. jecorina. We found that the photoreceptors BLR1 and BLR2 and the light-regulatory protein ENV1 have no effect on male fertility, while ENV1 is essential for female fertility. BLR1 and BLR2 were found to impact fruiting body formation although they are not essential for mating. Quantitative reverse transcription-PCR (qRT-PCR) analyses revealed that BLR1, BLR2, and ENV1 negatively regulate transcript levels of both pheromone receptors as well as peptide pheromone precursors in light but not in darkness and in a mating type-dependent manner. The effect of BLR1 and BLR2 on regulation of pheromone precursor and receptor genes is less severe than that of ENV1 as strains lacking env1 show 100-fold (for ppg1) to more than 100,000-fold (for hpp1) increased transcript levels of pheromone precursor genes as well as more than 20-fold increased levels of hpr1, the pheromone receptor receiving the HPP1 signal in a MAT1-1 strain. ENV1 likely integrates additional signals besides light, and our results indicate that its function is partially mediated via regulation of mat1-2-1. We conclude that ENV1 is essential for balancing the levels of genes regulated in a mating-type-dependent manner, which contributes to determination of sexual identity and fruiting body formation.
Collapse
|
43
|
Hunt S, Elvin M, Heintzen C. Temperature-sensitive and circadian oscillators of Neurospora crassa share components. Genetics 2012; 191:119-31. [PMID: 22367035 PMCID: PMC3338254 DOI: 10.1534/genetics.111.137976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 02/06/2012] [Indexed: 11/18/2022] Open
Abstract
In Neurospora crassa, the interactions between products of the frequency (frq), frequency-interacting RNA helicase (frh), white collar-1 (wc-1), and white collar-2 (wc-2) genes establish a molecular circadian clockwork, called the FRQ-WC-Oscillator (FWO), which is required for the generation of molecular and overt circadian rhythmicity. In strains carrying nonfunctional frq alleles, circadian rhythms in asexual spore development (conidiation) are abolished in constant conditions, yet conidiation remains rhythmic in temperature cycles. Certain characteristics of these temperature-synchronized rhythms have been attributed to the activity of a FRQ-less oscillator (FLO). The molecular components of this FLO are as yet unknown. To test whether the FLO depends on other circadian clock components, we created a strain that carries deletions in the frq, wc-1, wc-2, and vivid (vvd) genes. Conidiation in this ΔFWO strain was still synchronized to cyclic temperature programs, but temperature-induced rhythmicity was distinct from that seen in single frq knockout strains. These results and other evidence presented indicate that components of the FWO are part of the temperature-induced FLO.
Collapse
Affiliation(s)
- Suzanne Hunt
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Mark Elvin
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Christian Heintzen
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| |
Collapse
|
44
|
Schmoll M, Tian C, Sun J, Tisch D, Glass NL. Unravelling the molecular basis for light modulated cellulase gene expression - the role of photoreceptors in Neurospora crassa. BMC Genomics 2012; 13:127. [PMID: 22462823 PMCID: PMC3364853 DOI: 10.1186/1471-2164-13-127] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/31/2012] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. Studies with the biotechnological fungal workhorse Trichoderma reesei (Hypocrea jecorina) have revealed an interconnection between transcriptional regulation of cellulolytic enzymes and the light response. Neurospora crassa has been used as a model organism to study light and circadian rhythm biology. We therefore investigated whether light also regulates transcriptional regulation of cellulolytic enzymes in N. crassa. RESULTS We show that the N. crassa photoreceptor genes wc-1, wc-2 and vvd are involved in regulation of cellulase gene expression, indicating that this phenomenon is conserved among filamentous fungi. The negative effect of VVD on production of cellulolytic enzymes is thereby accomplished by its role in photoadaptation and hence its function in White collar complex (WCC) formation. In contrast, the induction of vvd expression by the WCC does not seem to be crucial in this process. Additionally, we found that WC-1 and WC-2 not only act as a complex, but also have individual functions upon growth on cellulose. CONCLUSIONS Genome wide transcriptome analysis of photoreceptor mutants and evaluation of results by analysis of mutant strains identified several candidate genes likely to play a role in light modulated cellulase gene expression. Genes with functions in amino acid metabolism, glycogen metabolism, energy supply and protein folding are enriched among genes with decreased expression levels in the wc-1 and wc-2 mutants. The ability to properly respond to amino acid starvation, i. e. up-regulation of the cross pathway control protein cpc-1, was found to be beneficial for cellulase gene expression. Our results further suggest a contribution of oxidative depolymerization of cellulose to plant cell wall degradation in N. crassa.
Collapse
Affiliation(s)
- Monika Schmoll
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
- Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Wien, Austria
| | - Chaoguang Tian
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jianping Sun
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
| | - Doris Tisch
- Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Wien, Austria
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
45
|
Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM. Comprehensive modelling of the Neurospora circadian clock and its temperature compensation. PLoS Comput Biol 2012; 8:e1002437. [PMID: 22496627 PMCID: PMC3320131 DOI: 10.1371/journal.pcbi.1002437] [Citation(s) in RCA: 27] [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: 09/29/2011] [Accepted: 02/06/2012] [Indexed: 11/19/2022] Open
Abstract
Circadian clocks provide an internal measure of external time allowing organisms to anticipate and exploit predictable daily changes in the environment. Rhythms driven by circadian clocks have a temperature compensated periodicity of approximately 24 hours that persists in constant conditions and can be reset by environmental time cues. Computational modelling has aided our understanding of the molecular mechanisms of circadian clocks, nevertheless it remains a major challenge to integrate the large number of clock components and their interactions into a single, comprehensive model that is able to account for the full breadth of clock phenotypes. Here we present a comprehensive dynamic model of the Neurospora crassa circadian clock that incorporates its key components and their transcriptional and post-transcriptional regulation. The model accounts for a wide range of clock characteristics including: a periodicity of 21.6 hours, persistent oscillation in constant conditions, arrhythmicity in constant light, resetting by brief light pulses, and entrainment to full photoperiods. Crucial components influencing the period and amplitude of oscillations were identified by control analysis. Furthermore, simulations enabled us to propose a mechanism for temperature compensation, which is achieved by simultaneously increasing the translation of frq RNA and decreasing the nuclear import of FRQ protein. Circadian clocks are internal timekeepers that integrate signals from the environment and orchestrate cellular events to occur at the most favourable time of day. Circadian clocks in animals, plants, fungi and bacteria have similar characteristic properties and molecular architecture. They have a periodicity of approximately 24 hours, persist in constant conditions and can be reset by environmental time cues such as light and temperature. Another essential property, whose molecular basis is poorly understood, is that the period is temperature compensated i.e. it remains the same over a range of temperatures. Computational modelling has become a valuable tool to predict and understand the underlying mechanisms of such complex molecular systems, but existing clock models are often restricted in the scope of molecular reactions they cover and in the breadth of conditions they are able to reproduce. We therefore built a comprehensive model of the circadian clock of the fungus Neurospora crassa, which encompasses existing knowledge of the biochemistry of the Neurospora clock. We validated this model against a wide range of experimental phenotypes and then used the model to investigate possible molecular explanations of temperature compensation. Our simulations suggest that temperature compensation of period is achieved by changing the abundance and cellular localisation of a key clock protein.
Collapse
Affiliation(s)
- Yu-Yao Tseng
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Suzanne M. Hunt
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Christian Heintzen
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Susan K. Crosthwaite
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail: (SKC); (JMS)
| | - Jean-Marc Schwartz
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail: (SKC); (JMS)
| |
Collapse
|
46
|
Dong JZ, Liu MR, Lei C, Zheng XJ, Wang Y. Effects of selenium and light wavelengths on liquid culture of Cordyceps militaris Link. Appl Biochem Biotechnol 2012; 166:2030-6. [PMID: 22434354 DOI: 10.1007/s12010-012-9628-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 02/22/2012] [Indexed: 11/24/2022]
Abstract
To investigate the effects of selenium and light wavelengths on the growth of liquid-cultured Cordyceps militaris and the main active components' accumulation, culture conditions as selenium selenite concentrations and light of different wavelengths were studied. The results are: adenosine accumulation proved to be significantly selenium dependent (R(2) = 0.9403) and cordycepin contents were determined to be not significantly selenium dependent (R(2) = 0.3845) but significantly enhanced by selenium except for 20 ppm; there were significant differences in cordycepin contents, adenosine contents, and mycelium growth caused by light wavelengths: cordycepin, blue light > pink light > daylight, darkness, red light; adenosine, red light > pink light, darkness, daylight, blue light; and mycelium growth, red light > pink light, darkness, daylight > blue light. In conclusion, light wavelength had a significant influence on production of mycelia, adenosine, and cordycepin, so lightening wavelength should be changed according to target products in the liquid culture of C. militaris.
Collapse
Affiliation(s)
- J Z Dong
- Key Laboratory of Biologic Resources Protection and Utilization of Hubei Province, School of Biological Science and Technology, Hubei University for Nationalities, Enshi, China.
| | | | | | | | | |
Collapse
|
47
|
Neurospora crassa Light Signal Transduction Is Affected by ROS. JOURNAL OF SIGNAL TRANSDUCTION 2011; 2012:791963. [PMID: 22046507 PMCID: PMC3199206 DOI: 10.1155/2012/791963] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 06/23/2011] [Indexed: 11/17/2022]
Abstract
In the ascomycete fungus Neurospora crassa blue-violet light controls the expression of genes responsible for differentiation of reproductive structures, synthesis of secondary metabolites, and the circadian oscillator activity. A major photoreceptor in Neurospora cells is WCC, a heterodimeric complex formed by the PAS-domain-containing polypeptides WC-1 and WC-2, the products of genes white collar-1 and white collar-2. The photosignal transduction is started by photochemical activity of an excited FAD molecule noncovalently bound by the LOV domain (a specialized variant of the PAS domain). The presence of zinc fingers (the GATA-recognizing sequences) in both WC-1 and WC-2 proteins suggests that they might function as transcription factors. However, a critical analysis of the phototransduction mechanism considers the existence of residual light responses upon absence of WCC or its homologs in fungi. The data presented
point at endogenous ROS generated by a photon stimulus as an alternative input to pass on light signals to downstream targets.
Collapse
|
48
|
Abstract
Circadian clocks organize our inner physiology with respect to the external world, providing life with the ability to anticipate and thereby better prepare for major fluctuations in its environment. Circadian systems are widely represented in nearly all major branches of life, except archaebacteria, and within the eukaryotes, the filamentous fungus Neurospora crassa has served for nearly half a century as a durable model organism for uncovering the basic circadian physiology and molecular biology. Studies using Neurospora have clarified our fundamental understanding of the clock as nested positive and negative feedback loops regulated through transcriptional and post-transcriptional processes. These feedback loops are centered on a limited number of proteins that form molecular complexes, and their regulation provides a physical explanation for nearly all clock properties. This review will introduce the basics of circadian rhythms, the model filamentous fungus N. crassa, and provide an overview of the molecular components and regulation of the circadian clock.
Collapse
|
49
|
Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC. CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genet 2011; 7:e1002166. [PMID: 21811413 PMCID: PMC3140994 DOI: 10.1371/journal.pgen.1002166] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/18/2011] [Indexed: 12/21/2022] Open
Abstract
Circadian-regulated gene expression is predominantly controlled by a transcriptional negative feedback loop, and it is evident that chromatin modifications and chromatin remodeling are integral to this process in eukaryotes. We previously determined that multiple ATP-dependent chromatin-remodeling enzymes function at frequency (frq). In this report, we demonstrate that the Neurospora homologue of chd1 is required for normal remodeling of chromatin at frq and is required for normal frq expression and sustained rhythmicity. Surprisingly, our studies of CHD1 also revealed that DNA sequences within the frq promoter are methylated, and deletion of chd1 results in expansion of this methylated domain. DNA methylation of the frq locus is altered in strains bearing mutations in a variety of circadian clock genes, including frq, frh, wc-1, and the gene encoding the frq antisense transcript (qrf). Furthermore, frq methylation depends on the DNA methyltransferase, DIM-2. Phenotypic characterization of Δdim-2 strains revealed an approximate WT period length and a phase advance of approximately 2 hours, indicating that methylation plays only an ancillary role in clock-regulated gene expression. This suggests that DNA methylation, like the antisense transcript, is necessary to establish proper clock phasing but does not control overt rhythmicity. These data demonstrate that the epigenetic state of clock genes is dependent on normal regulation of clock components.
Collapse
Affiliation(s)
- William J. Belden
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Zachary A. Lewis
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Eric U. Selker
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Jennifer J. Loros
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Jay C. Dunlap
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- * E-mail:
| |
Collapse
|
50
|
Zhang R, Xiao T, Hou Z. Internal noise enhanced oscillation in a delayed circadian pacemaker. Biophys Chem 2011; 158:54-60. [PMID: 21605935 DOI: 10.1016/j.bpc.2011.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 04/28/2011] [Accepted: 05/01/2011] [Indexed: 10/18/2022]
Abstract
The effect of internal noise in a delayed circadian oscillator is studied by using both chemical Langevin equations and stochastic normal form theory. It is found that internal noise can induce circadian oscillation even if the delay time τ is below the deterministic Hopf bifurcation τ(h). We use signal-to-noise ratio (SNR) to quantitatively characterize the performance of such noise induced oscillations and a threshold value of SNR is introduced to define the so-called effective oscillation. Interestingly, the τ-range for effective stochastic oscillation, denoted as Δτ(EO), shows a bell-shaped dependence on the intensity of internal noise which is inversely proportional to the system size. We have also investigated how the rates of synthesis and degradation of the clock protein influence the SNR and thus Δτ(EO). The decay rate K(d) could significantly affect Δτ(EO), while varying the gene expression rate K(e) has no obvious effect if K(e) is not too small. Stochastic normal form analysis and numerical simulations are in good consistency with each other. This work provides us comprehensive understandings of how internal noise and time delay work cooperatively to influence the dynamics of circadian oscillations.
Collapse
Affiliation(s)
- Ruiting Zhang
- Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Anhui, China
| | | | | |
Collapse
|