1
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Westgeest AJ, Dauzat M, Simonneau T, Pantin F. Leaf starch metabolism sets the phase of stomatal rhythm. THE PLANT CELL 2023; 35:3444-3469. [PMID: 37260348 PMCID: PMC10473205 DOI: 10.1093/plcell/koad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
In leaves of C3 and C4 plants, stomata open during the day to favor CO2 entry for photosynthesis and close at night to prevent inefficient transpiration of water vapor. The circadian clock paces rhythmic stomatal movements throughout the diel (24-h) cycle. Leaf transitory starch is also thought to regulate the diel stomatal movements, yet the underlying mechanisms across time (key moments) and space (relevant leaf tissues) remain elusive. Here, we developed PhenoLeaks, a pipeline to analyze the diel dynamics of transpiration, and used it to screen a series of Arabidopsis (Arabidopsis thaliana) mutants impaired in starch metabolism. We detected a sinusoidal, endogenous rhythm of transpiration that overarches days and nights. We determined that a number of severe mutations in starch metabolism affect the endogenous rhythm through a phase shift, resulting in delayed stomatal movements throughout the daytime and diminished stomatal preopening during the night. Nevertheless, analysis of tissue-specific mutations revealed that neither guard-cell nor mesophyll-cell starch metabolisms are strictly required for normal diel patterns of transpiration. We propose that leaf starch influences the timing of transpiration rhythm through an interplay between the circadian clock and sugars across tissues, while the energetic effect of starch-derived sugars is usually nonlimiting for endogenous stomatal movements.
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Affiliation(s)
| | - Myriam Dauzat
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | - Florent Pantin
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers F-49000, France
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2
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Hughes FA, Barr AR, Thomas P. Patterns of interdivision time correlations reveal hidden cell cycle factors. eLife 2022; 11:e80927. [PMID: 36377847 PMCID: PMC9822260 DOI: 10.7554/elife.80927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
The time taken for cells to complete a round of cell division is a stochastic process controlled, in part, by intracellular factors. These factors can be inherited across cellular generations which gives rise to, often non-intuitive, correlation patterns in cell cycle timing between cells of different family relationships on lineage trees. Here, we formulate a framework of hidden inherited factors affecting the cell cycle that unifies known cell cycle control models and reveals three distinct interdivision time correlation patterns: aperiodic, alternator, and oscillator. We use Bayesian inference with single-cell datasets of cell division in bacteria, mammalian and cancer cells, to identify the inheritance motifs that underlie these datasets. From our inference, we find that interdivision time correlation patterns do not identify a single cell cycle model but generally admit a broad posterior distribution of possible mechanisms. Despite this unidentifiability, we observe that the inferred patterns reveal interpretable inheritance dynamics and hidden rhythmicity of cell cycle factors. This reveals that cell cycle factors are commonly driven by circadian rhythms, but their period may differ in cancer. Our quantitative analysis thus reveals that correlation patterns are an emergent phenomenon that impact cell proliferation and these patterns may be altered in disease.
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Affiliation(s)
- Fern A Hughes
- Department of Mathematics, Imperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
| | - Alexis R Barr
- MRC London Institute of Medical SciencesLondonUnited Kingdom
- Institute of Clinical Sciences, Imperial College LondonLondonUnited Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College LondonLondonUnited Kingdom
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3
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Decomposing biophotovoltaic current density profiles using the Hilbert-Huang transform reveals influences of circadian clock on cyanobacteria exoelectrogenesis. Sci Rep 2022; 12:10962. [PMID: 35768500 PMCID: PMC9243294 DOI: 10.1038/s41598-022-15111-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 04/14/2022] [Indexed: 11/21/2022] Open
Abstract
Electrons from cyanobacteria photosynthetic and respiratory systems are implicated in current generated in biophotovoltaic (BPV) devices. However, the pathway that electrons follow to electrodes remains largely unknown, limiting progress of applied research. Here we use Hilbert–Huang Transforms to decompose Synechococcus elongatus sp. PCC7942 BPV current density profiles into physically meaningful oscillatory components, and compute their instantaneous frequencies. We develop hypotheses for the genesis of the oscillations via repeat experiments with iron-depleted and 20% CO\documentclass[12pt]{minimal}
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\begin{document}$${_2}$$\end{document}2 enriched biofilms. The oscillations exhibit rhythms that are consistent with the state of the art cyanobacteria circadian model, and putative exoelectrogenic pathways. In particular, we observe oscillations consistent with: rhythmic D1:1 (photosystem II core) expression; circadian-controlled glycogen accumulation; circadian phase shifts under modified intracellular %ATP; and circadian period shortening in the absence of the iron-sulphur protein LdpA. We suggest that the extracted oscillations may be used to reverse-identify proteins and/or metabolites responsible for cyanobacteria exoelectrogenesis.
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4
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Shinde S, Singapuri S, Jiang Z, Long B, Wilcox D, Klatt C, Jones JA, Yuan JS, Wang X. Thermodynamics contributes to high limonene productivity in cyanobacteria. Metab Eng Commun 2022; 14:e00193. [PMID: 35145855 PMCID: PMC8801761 DOI: 10.1016/j.mec.2022.e00193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 01/02/2023] Open
Abstract
Terpenoids are a large group of secondary metabolites with broad industrial applications. Engineering cyanobacteria is an attractive route for the sustainable production of commodity terpenoids. Currently, a major obstacle lies in the low productivity attained in engineered cyanobacterial strains. Traditional metabolic engineering to improve pathway kinetics has led to limited success in enhancing terpenoid productivity. In this study, we reveal thermodynamics as the main determinant for high limonene productivity in cyanobacteria. Through overexpressing the primary sigma factor, a higher photosynthetic rate was achieved in an engineered strain of Synechococcus elongatus PCC 7942. Computational modeling and wet lab analyses showed an increased flux toward both native carbon sink glycogen synthesis and the non-native limonene synthesis from photosynthate output. On the other hand, comparative proteomics showed decreased expression of terpene pathway enzymes, revealing their limited role in determining terpene flux. Lastly, growth optimization by enhancing photosynthesis has led to a limonene titer of 19 mg/L in 7 days with a maximum productivity of 4.3 mg/L/day. This study highlights the importance of enhancing photosynthesis and substrate input for the high productivity of secondary metabolic pathways, providing a new strategy for future terpenoid engineering in phototrophs. Pathway enzyme engineering marginally increases cyanobacterial terpene production. Sigma factor overexpression improves photosynthetic efficiency in cyanobacteria. Enhanced photosynthesis results in high limonene production in cyanobacteria. Enhanced photosynthesis provides high thermodynamic driving force for terpenes.
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Affiliation(s)
- Shrameeta Shinde
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA
| | - Sonali Singapuri
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA
| | - Zhenxiong Jiang
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA
| | - Bin Long
- Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Danielle Wilcox
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA
| | - Camille Klatt
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA
| | - J. Andrew Jones
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Joshua S. Yuan
- Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Xin Wang
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA
- Corresponding author.
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5
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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6
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Guo JH, Ma XH, Ma H, Zhang Y, Tian ZQ, Wang X, Shao YC. Circadian misalignment on submarines and other non-24-h environments - from research to application. Mil Med Res 2020; 7:39. [PMID: 32814592 PMCID: PMC7437048 DOI: 10.1186/s40779-020-00268-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 08/10/2020] [Indexed: 11/10/2022] Open
Abstract
Circadian clocks have important physiological and behavioral functions in humans and other organisms, which enable organisms to anticipate and respond to periodic environmental changes. Disturbances in circadian rhythms impair sleep, metabolism, and behavior. People with jet lag, night workers and shift workers are vulnerable to circadian misalignment. In addition, non-24-h cycles influence circadian rhythms and cause misalignment and disorders in different species, since these periods are beyond the entrainment ranges. In certain special conditions, e.g., on submarines and commercial ships, non-24-h watch schedules are often employed, which have also been demonstrated to be deleterious to circadian rhythms. Personnel working under such conditions suffer from circadian misalignment with their on-watch hours, leading to increased health risks and decreased cognitive performance. In this review, we summarize the research progress and knowledge concerning circadian rhythms on submarines and other environments in which non-24-h watch schedules are employed.
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Affiliation(s)
- Jin-Hu Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Xiao-Hong Ma
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Huan Ma
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yin Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhi-Qiang Tian
- China Institute of Marine Technology and Economy, Beijing, 100081, China
| | - Xin Wang
- China Institute of Marine Technology and Economy, Beijing, 100081, China
| | - Yong-Cong Shao
- School of Psychology, Beijing Sport University, Beijing, 100084, China
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7
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Smith LM, Motta FC, Chopra G, Moch JK, Nerem RR, Cummins B, Roche KE, Kelliher CM, Leman AR, Harer J, Gedeon T, Waters NC, Haase SB. An intrinsic oscillator drives the blood stage cycle of the malaria parasite Plasmodium falciparum. Science 2020; 368:754-759. [PMID: 32409472 DOI: 10.1126/science.aba4357] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/11/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The blood stage of the infection of the malaria parasite Plasmodium falciparum exhibits a 48-hour developmental cycle that culminates in the synchronous release of parasites from red blood cells, which triggers 48-hour fever cycles in the host. This cycle could be driven extrinsically by host circadian processes or by a parasite-intrinsic oscillator. To distinguish between these hypotheses, we examine the P. falciparum cycle in an in vitro culture system and show that the parasite has molecular signatures associated with circadian and cell cycle oscillators. Each of the four strains examined has a different period, which indicates strain-intrinsic period control. Finally, we demonstrate that parasites have low cell-to-cell variance in cycle period, on par with a circadian oscillator. We conclude that an intrinsic oscillator maintains Plasmodium's rhythmic life cycle.
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Affiliation(s)
| | - Francis C Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Garima Chopra
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - J Kathleen Moch
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Robert R Nerem
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Bree Cummins
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Kimberly E Roche
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | | | - Adam R Leman
- Department of Biology, Duke University, Durham, NC, USA
| | - John Harer
- Department of Mathematics, Duke University, Durham, NC, USA
| | - Tomas Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Norman C Waters
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Steven B Haase
- Department of Biology, Duke University, Durham, NC, USA. .,Department of Medicine, Duke University, Durham, NC, USA
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8
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The recovery of KaiA’s activity depends on its N-terminal domain and KaiB in the cyanobacterial circadian clock. Biochem Biophys Res Commun 2020; 524:123-128. [DOI: 10.1016/j.bbrc.2020.01.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/13/2020] [Indexed: 11/20/2022]
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9
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Genov N, Castellana S, Scholkmann F, Capocefalo D, Truglio M, Rosati J, Turco EM, Biagini T, Carbone A, Mazza T, Relógio A, Mazzoccoli G. A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics. Int J Mol Sci 2019; 20:ijms20184585. [PMID: 31533246 PMCID: PMC6770795 DOI: 10.3390/ijms20184585] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/27/2022] Open
Abstract
Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components.
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Affiliation(s)
- Nikolai Genov
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 1011 Berlin, Germany.
- Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany.
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Felix Scholkmann
- Research Office for Complex Physical and Biological Systems (ROCoS), 8006 Zurich, Switzerland.
- Department of Neonatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland.
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Mauro Truglio
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Jessica Rosati
- Cell Reprogramming Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Elisa Maria Turco
- Cell Reprogramming Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Annalucia Carbone
- Division of Internal Medicine and Chronobiology Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 1011 Berlin, Germany.
- Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany.
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
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10
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Tokuda IT, Akman OE, Locke JCW. Reducing the complexity of mathematical models for the plant circadian clock by distributed delays. J Theor Biol 2018; 463:155-166. [PMID: 30550861 DOI: 10.1016/j.jtbi.2018.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 11/29/2022]
Abstract
A major bottleneck in the modelling of biological networks is the parameter explosion problem - the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently - reducing the number of parameters - whilst still preserving the core mechanistic dynamics of the gene regulatory network. Compared to models with discrete time-delays, which are governed by functional differential equations, the distributed delay models can be converted into sets of equivalent ordinary differential equations, enabling the use of standard methods for numerical integration, and for stability and bifurcation analyses. We demonstrate the efficiency of our modelling approach by applying it to three exemplar mathematical models of the Arabidopsis circadian clock of varying complexity, obtaining significant reductions in complexity in each case. Moreover, we revise one of the most up-to-date Arabidopsis models, updating the regulation of the PRR9 and PRR7 genes by LHY in accordance with recent experimental data. The revised model more accurately reproduces the LHY-induction experiments of core clock genes, compared with the original model. Our work thus shows that the method of distributed delays facilitates the optimisation and reformulation of genetic network models.
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Affiliation(s)
- Isao T Tokuda
- Graduate School of Science and Engineering, Ritsumeikan University, Noji-higashi, Kusatsu, Shiga 525-8577, Japan.
| | - Ozgur E Akman
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK.
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK.
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11
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Fleming KE, O’Shea EK. An RpaA-Dependent Sigma Factor Cascade Sets the Timing of Circadian Transcriptional Rhythms in Synechococcus elongatus. Cell Rep 2018; 25:2937-2945.e3. [DOI: 10.1016/j.celrep.2018.11.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/31/2018] [Accepted: 11/12/2018] [Indexed: 10/27/2022] Open
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12
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Martins BMC, Tooke AK, Thomas P, Locke JCW. Cell size control driven by the circadian clock and environment in cyanobacteria. Proc Natl Acad Sci U S A 2018; 115:E11415-E11424. [PMID: 30409801 PMCID: PMC6275512 DOI: 10.1073/pnas.1811309115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light-dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.
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Affiliation(s)
- Bruno M C Martins
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Amy K Tooke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College London, SW7 2AZ London, United Kingdom
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom;
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13
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Martins BMC, Tooke AK, Thomas P, Locke JCW. Cell size control driven by the circadian clock and environment in cyanobacteria. Proc Natl Acad Sci U S A 2018. [PMID: 30409801 DOI: 10.1002/(sici)1521-1878(200001)22:1¡10::aid-bies4¿3.0.co;2-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light-dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.
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Affiliation(s)
- Bruno M C Martins
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Amy K Tooke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College London, SW7 2AZ London, United Kingdom
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom;
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14
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Joanito I, Chu JW, Wu SH, Hsu CP. An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states. Sci Rep 2018; 8:13944. [PMID: 30224713 PMCID: PMC6141573 DOI: 10.1038/s41598-018-32030-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
In higher plants (e.g., Arabidopsis thaliana), the core structure of the circadian clock is mostly governed by a repression process with very few direct activators. With a series of simplified models, we studied the underlying mechanism and found that the Arabidopsis clock consists of type-2 incoherent feed-forward loops (IFFLs), one of them creating a pulse-like expression in PRR9/7. The double-negative feedback loop between CCA1/LHY and PRR5/TOC1 generates a bistable, hysteretic behavior in the Arabidopsis circadian clock. We found that the IFFL involving PRR9/7 breaks the bistability and moves the system forward with a rapid pulse in the daytime, and the evening complex (EC) breaks it in the evening. With this illustration, we can intuitively explain the behavior of the clock under mutant conditions. Thus, our results provide new insights into the underlying network structures of the Arabidopsis core oscillator.
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Affiliation(s)
- Ignasius Joanito
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Jhih-Wei Chu
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.
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15
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Castellana S, Mazza T, Capocefalo D, Genov N, Biagini T, Fusilli C, Scholkmann F, Relógio A, Hogenesch JB, Mazzoccoli G. Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes. Front Physiol 2018; 9:1178. [PMID: 30190679 PMCID: PMC6115496 DOI: 10.3389/fphys.2018.01178] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/06/2018] [Indexed: 02/02/2023] Open
Abstract
In living organisms, biological clocks regulate 24 h (circadian) molecular, physiological, and behavioral rhythms to maintain homeostasis and synchrony with predictable environmental changes, in particular with those induced by Earth’s rotation on its axis. Harmonics of these circadian rhythms having periods of 8 and 12 h (ultradian) have been documented in several species. In mouse liver, harmonics of the 24-h period of gene transcription hallmarked genes oscillating with a frequency two or three times faster than circadian periodicity. Many of these harmonic transcripts enriched pathways regulating responses to environmental stress and coinciding preferentially with subjective dawn and dusk. At this time, the evolutionary history of genes with rhythmic expression is still poorly known and the role of length-of-day changes due to Earth’s rotation speed decrease over the last four billion years is totally ignored. We hypothesized that ultradian and stress anticipatory genes would be more evolutionarily conserved than circadian genes and background non-oscillating genes. To investigate this issue, we performed broad computational analyses of genes/proteins oscillating at different frequency ranges across several species and showed that ultradian genes/proteins, especially those oscillating with a 12-h periodicity, are more likely to be of ancient origin and essential in mice. In summary, our results show that genes with ultradian transcriptional patterns are more likely to be phylogenetically conserved and associated with the primeval and inevitable dawn/dusk transitions.
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Affiliation(s)
- Stefano Castellana
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Nikolai Genov
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin and Humboldt University of Berlin, Berlin, Germany.,Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Felix Scholkmann
- Research Office for Complex Physical and Biological Systems (ROCoS), Zürich, Switzerland.,Department of Neonatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin and Humboldt University of Berlin, Berlin, Germany.,Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - John B Hogenesch
- Divisions of Human Genetics and Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
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16
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van Heerden JH, Kempe H, Doerr A, Maarleveld T, Nordholt N, Bruggeman FJ. Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli. Sci Rep 2017; 7:16094. [PMID: 29170466 PMCID: PMC5700928 DOI: 10.1038/s41598-017-15895-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022] Open
Abstract
The inherent stochasticity of molecular reactions prevents us from predicting the exact state of single-cells in a population. However, when a population grows at steady-state, the probability to observe a cell with particular combinations of properties is fixed. Here we validate and exploit existing theory on the statistics of single-cell growth in order to predict the probability of phenotypic characteristics such as cell-cycle times, volumes, accuracy of division and cell-age distributions, using real-time imaging data for Bacillus subtilis and Escherichia coli. Our results show that single-cell growth-statistics can accurately be predicted from a few basic measurements. These equations relate different phenotypic characteristics, and can therefore be used in consistency tests of experimental single-cell growth data and prediction of single-cell statistics. We also exploit these statistical relations in the development of a fast stochastic-simulation algorithm of single-cell growth and protein expression. This algorithm greatly reduces computational burden, by recovering the statistics of growing cell-populations from the simulation of only one of its lineages. Our approach is validated by comparison of simulations and experimental data. This work illustrates a methodology for the prediction, analysis and tests of consistency of single-cell growth and protein expression data from a few basic statistical principles.
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Affiliation(s)
- Johan H van Heerden
- Systems Bioinformatics, VU University, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands
| | - Hermannus Kempe
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Anne Doerr
- Systems Bioinformatics, VU University, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, TU Delft, Delft, The Netherlands
| | - Timo Maarleveld
- Systems Bioinformatics, VU University, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands
- Central Risk Management, ABN AMRO NV, Amsterdam, The Netherlands
| | - Niclas Nordholt
- Systems Bioinformatics, VU University, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands
- Federal Institute for Materials Research and Testing (Department of Materials and Environment, Division Biodeterioration and Reference Organisms), D-12205, Berlin, Germany
| | - Frank J Bruggeman
- Systems Bioinformatics, VU University, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands.
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17
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Kang JH, Cho KH. A novel interaction perturbation analysis reveals a comprehensive regulatory principle underlying various biochemical oscillators. BMC SYSTEMS BIOLOGY 2017; 11:95. [PMID: 29017496 PMCID: PMC5635494 DOI: 10.1186/s12918-017-0472-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/02/2017] [Indexed: 02/05/2023]
Abstract
Background Biochemical oscillations play an important role in maintaining physiological and cellular homeostasis in biological systems. The frequency and amplitude of oscillations are regulated to properly adapt to environments by numerous interactions within biomolecular networks. Despite the advances in our understanding of biochemical oscillators, the relationship between the network structure of an oscillator and its regulatory function still remains unclear. To investigate such a relationship in a systematic way, we have developed a novel analysis method called interaction perturbation analysis that enables direct modulation of the strength of every interaction and evaluates its consequence on the regulatory function. We have applied this new method to the analysis of three representative types of oscillators. Results The results of interaction perturbation analysis showed different regulatory features according to the network structure of the oscillator: (1) both frequency and amplitude were seldom modulated in simple negative feedback oscillators; (2) frequency could be tuned in amplified negative feedback oscillators; (3) amplitude could be modulated in the incoherently amplified negative feedback oscillators. A further analysis of naturally-occurring biochemical oscillator models supported such different regulatory features according to their network structures. Conclusions Our results provide a clear evidence that different network structures have different regulatory features in modulating the oscillation frequency and amplitude. Our findings may help to elucidate the fundamental regulatory roles of network structures in biochemical oscillations. Electronic supplementary material The online version of this article (10.1186/s12918-017-0472-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Hyuk Kang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea. .,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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18
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Maheshwari K, Srivastava MK, Saxena S, Jain A. Effect of fluorinated/non-fluorinated β-diketones and side-chain branching of N-protected amino acids on the antibacterial potential of new heptacoordinated monobutyltin(IV) complexes. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.3628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Karuna Maheshwari
- Department of Chemistry; University of Rajasthan; Jaipur 302004 India
| | | | - Sanjiv Saxena
- Department of Chemistry; University of Rajasthan; Jaipur 302004 India
| | - Asha Jain
- Department of Chemistry; University of Rajasthan; Jaipur 302004 India
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19
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Abstract
Organisms use circadian clocks to generate 24‐h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these different frequencies are generated. Here, we examine this problem by studying the coupling of the clock to the alternative sigma factor sigC in the cyanobacterium Synechococcus elongatus. Using single‐cell microscopy, we find that psbAI, a key photosynthesis gene regulated by both sigC and the clock, is activated with two peaks of gene expression every circadian cycle under constant low light. This two‐peak oscillation is dependent on sigC, without which psbAI rhythms revert to one oscillatory peak per day. We also observe two circadian peaks of elongation rate, which are dependent on sigC, suggesting a role for the frequency doubling in modulating growth. We propose that the two‐peak rhythm in psbAI expression is generated by an incoherent feedforward loop between the clock, sigC and psbAI. Modelling and experiments suggest that this could be a general network motif to allow frequency doubling of outputs.
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Affiliation(s)
| | - Arijit K Das
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Liliana Antunes
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - James Cw Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK .,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Microsoft Research, Cambridge, UK
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