Circadian rhythms in bacteria and microbiomes / / Carl Hirschie Johnson and Michael Joseph Rust (editors)

• Record Nr.: UNINA9910485606103321
• Pubbl/distr/stampa: Cham, Switzerland : , : Springer, , [2021]; ©2021
• ISBN: 3-030-72158-2
• Descrizione fisica: 1 online resource (424 pages)
• Disciplina: 579.3
• Soggetti: Prokaryotes; Circadian rhythms; Procariotes; Ritmes circadiaris; Llibres electrònics
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Nota di bibliografia: Includes bibliographical references.
• Nota di contenuto: Intro -- Dedications -- Dedication to Dr. Carol Rae Andersson (May 5, 1965-January 24, 2009) She left us too soon! -- Dedication to Dr. Yohko Kitayama (1976-2016) -- To Takao Kondo on the Occasion of His Retirement -- Acknowledgments -- References -- Preface -- Contents -- The Bacterial Perspective on Circadian Clocks -- 1 The ``No Clocks in Proks´´ Dogma -- 2 Data Dethroned the Dogma: Circadian Rhythms in Cyanobacteria -- 3 Establishing the Synechococcus elongatus PCC 7942 Model System -- References -- Part I: The Circadian Clock System in Cyanobacteria: Pioneer of Bacterial Clocks -- Around the Circadian Clock: Review and Preview -- 1 With Duckweed -- 2 At the National Institute for Basic Biology -- 3 Plant Physiology -- 4 Cloning of the per Gene -- 5 Phototaxis of Chlamydomonas reinhardtii -- 6 Sabbatical: Toward a New Experimental System for Circadian Clocks -- 7 Meeting Dr. Susan Golden -- 8 Whispers of Bioluminescence -- 9 Japan-USA Joint Research -- 10 Design and Fabrication of Bioluminescence Measurement System -- 11 Development of LCM and LCA: With Inside Macintosh -- 12 Mutant Screening and Complementation by Library -- ; 13 Discovery of the KaiABC Clock Gene Cluster -- 14 Return to Nagoya University -- 15 What ``Not to Do´´ -- 16 Cyanobacterial Transcription and Translation Model: Central Dogma in a Loop? -- 17 Obligate Photoautotrophy: Key to the Circadian Paradox -- 18 Reconstitution Experiment -- 19 Perfect Circadian Oscillation -- 20 The CI-ATPase Activity of KaiC Determines the Period -- 21 Review and Preview -- 22 Inside KaiC -- 23 Harmonic and Relaxation Oscillation -- 24 About Mechanical Clocks -- 25 Dual ATPases Coupling Model for KaiC Circadian Oscillator -- 26 ATPase Measurement -- 27 What Is the ``Tension that Determines the Period?´´ -- 28 Fundamental Frequency Problem -- 29 Acknowledgment -- 30 Editors´ Note.; A Retrospective: On Disproving the Transcription-Translation Feedback Loop Model in Cyanobacteria -- 1 Transcription-Translation Feedback Loop Model -- 2 Beyond the TTFL Model -- 3 Establishment of the In Vitro Reconstitution System -- References -- Mechanistic Aspects of the Cyanobacterial Circadian Clock -- Bibliography -- Mechanism of the Cyanobacterial Circadian Clock Protein KaiC to Measure 24 Hours -- 1 Introduction -- 2 Clock Systems of Cyanobacteria -- 3 Characteristics of the Circadian Clock in Terms of Temperature Compensation of Period -- 4 ATPase Activity and Intramolecular Feedback of KaiC -- 5 Stable Circadian Oscillations Due to Interactions Between Two ATPase Domains of KaiC -- 6 Design of Mechanical Clocks and the Design of Circadian Clocks -- 7 Conclusions -- References -- Oscillation and Input Compensation in the Cyanobacterial Kai Proteins -- 1 The Cyanobacterial Oscillator as a Biochemical Model for Chronobiology -- 2 Phenomenology of the Cyanobacterial Oscillator -- 3 Metabolic Input and Input Compensation -- 4 Phase Plane Picture of Input Compensation and Entrainment -- 5 A Toy Model with Integral Feedback Can Decouple Period and Amplitude -- 6 Period and Amplitude in the Model -- 7 Does KaiC Phosphorylation Implement Integral Feedback? -- 8 Coexistence of a Stable Fixed Point and a Limit Cycle -- 9 Conclusion -- References -- Insights into the Evolution of Circadian Clocks Gleaned from Bacteria -- 1 Evolution of Circadian Clocks: What Can Bacterial Clocks Tell Us? -- 2 General Considerations Concerning the Evolutionary Significance of Clocks -- 3 How and Why Did Bacteria Evolve Circadian Timekeepers? -- 4 Self-Sustained Versus Damped Oscillators Versus Hourglass Timers -- 5 Testing Whether Clocks Are Adaptive -- 6 Competition Experiments and Assessment of Fitness -- 7 ``It Takes a Village:´´ Communities and Populations.; 8 A Medically Important Community: The Mammalian Gut Microbiome -- 9 Clocks Are Still Evolving! -- References -- Reasons for Seeking Information on the Molecular Structure and Dynamics of Circadian Clock Components in Cyanobacteria -- 1 Introduction -- 2 Narrowing a Research Question -- 3 Transmural Hierarchy -- 4 Structural Basis of Slowness in KaiC -- 5 From Intra- to Inter-Molecular Scales -- 6 Concluding Remarks -- References -- Single-Molecule Methods Applied to Circadian Proteins with Special Emphasis on Atomic Force Microscopy -- 1 Introduction -- 2 Single-Molecule Techniques -- 2.1 Single-Channel Patch-Clamp Recording -- 2.2 Single-Molecule Fluorescence Microscopy -- 2.3 Atomic Force Microscopy -- 2.3.1 HS-AFM Imaging -- 3 Visualizing Circadian Clock Proteins by HS-AFM -- 3.1 Experimental Conditions for HS-AFM Imaging of Kai Proteins -- 3.2 KaiA-KaiC Interaction -- 3.2.1 KaiA Interaction Depends upon KaiC Phosphostatus -- 3.2.2 Synchronous Oscillation of KaiA-KaiC Affinities with In Vitro Rhythm -- 3.2.3 Reinforcement of Oscillatory Resilience with PDDA -- 3.2.4 C-Terminal Tentacles of KaiC Hexamer Co-Operationally Bind to KaiA Dimer -- 3.3 KaiB-KaiC Interaction -- 3.3.1 ; Cooperative Binding of KaiB Monomers to KaiC Hexamer -- 3.3.2 KaiB Interaction Depends upon KaiC Phosphostatus -- 3.4 Visualization of KaiA-KaiB-KaiC Ternary Complex -- 4 Concluding Remarks -- References -- Diversity of Timing Systems in Cyanobacteria and Beyond -- 1 Introduction -- 2 Bioinformatics Analyses Reveal Diversity of Putative Clock Components in Cyanobacteria -- 2.1 The KaiABC Oscillator -- 2.2 The Circadian Protein Network Embedding the Core Clock -- 3 The Hourglass Timer -- 4 Synechocystis sp. PCC 6803: An Example of a Cyanobacterium Harboring Multiple Kai Homologs -- 4.1 Input and Output Pathways -- 4.2 The KaiB3C3 System.; 4.3 Manipulation of Clock Components as a Strategy to Switch Metabolic Routes -- 5 Potential KaiC-Based Timing Systems Outside Cyanobacteria -- 6 Conclusion -- References -- An In Vitro Approach to Elucidating Clock-Modulating Metabolites -- 1 Basics of the Circadian-Oscillating KaiC Phosphorylation -- 2 Modulating the Circadian Clock with Adenosine Diphosphate (ADP) -- 3 Resetting the Clock Through Sensing the Redox State of Quinone -- 4 Regulating the KaiC Autokinase and Autophosphatase Activities with Mg2+ -- 5 Keeping Time with KaiC Alone as an Hourglass -- 6 Future Perspectives -- References -- Damped Oscillation in the Cyanobacterial Clock System -- 1 Introduction -- 2 Hopf Bifurcation Is a Scenario for Emerging Damped Oscillations -- 3 Low-Temperature MAKES In Vitro Rhythms Dampen Through Hopf Bifurcation -- 4 Resonance of the Damped Oscillation of KaiC During Temperature Cycles -- 5 Damped Oscillation in the Absence of KaiA -- 6 Evolution of Self-Sustained Oscillation -- 7 Summary -- References -- Roles of Phosphorylation of KaiC in the Cyanobacterial Circadian Clock -- 1 Introduction -- 2 Discovery of KaiC Phosphorylation -- 3 Relationship Between KaiC Phosphorylation and the Interaction Among Kai Proteins -- 4 ATP-Binding Sites Located at the Subunit Interfaces of KaiC Hexamer -- 5 In Vitro Reconstitution of a Circadian Oscillator -- 6 Sequential Phosphorylation of S431 and T432 -- 7 Discovery of ATPase Activity of KaiC -- 8 An Unusual Mechanism of KaiC Autodephosphorylation -- 9 Structural Basis for Time-Specific Interactions Among Kai Proteins -- 10 A Link Between KaiC Phosphorylation and Circadian Gene Expression -- 11 Multiple Output Systems of the Protein-Based Oscillator -- 12 Perspective -- References -- Reprogramming Metabolic Networks and Manipulating Circadian Clocks for Biotechnological Applications -- 1 Introduction.; 2 Model Cyanobacterial Strains -- 3 Synthetic and Systems Biology in Cyanobacteria -- 4 Cyanobacterial Biofuels and Chemicals -- 4.1 Derivatives from Sugar Phosphates -- 4.2 Derivatives from DHAP -- 4.3 Derivatives from Pyruvate -- 4.4 Derivatives from Acetyl-CoA -- 4.5 Derivatives from TCA Cycle Metabolites -- 4.6 Derivatives from Amino Acids -- 4.7 Biomass Conversion -- 5 Modification of Cyanobacterial Framework for Improved Performance -- 5.1 Enhancing Photosynthetic Efficiency -- 5.2 Improving Carbon Assimilation -- 5.3 Rewiring the Central Carbon Metabolism -- 6 The Circadian Clock Regulates Gene Expression and Metabolism in Wild-Type Cyanobacteria -- 6.1 The Circadian Clock Governs Oscillation of Glycogen Content -- 6.2 The Circadian Oscillator Regulates Global Gene Expression and Metabolism -- 7 Global Complementary Regulation of Gene Expression Via Manipulation of the Clock -- 8 Manipulation of the Circadian Clock for Enhancing Expression of Foreign Genes -- 9 Conclusions and Prospects -- References -- Insights from Mathematical Modeling/Simulations of the In Vitro KaiABC Clock -- 1 Introduction -- 2 Insights from Simplified Phosphoform Dynamic Models -- 3 Hexamer Models and Allosteric Transitions -- References -- Part II: Circadian Phenomena in ; Microbiomes/Populations and Bacteria Besides Cyanobacteria -- Basic Biology of Rhythms and the Microbiome -- 1 Introduction -- 1.1 Circadian Rhythms in Mammals -- 1.2 Diurnal Rhythms of the Mammalian Microbiota -- 2 Circadian System in Host-Microbiome Interactions -- 2.1 Host Factors Shaping Microbiota Rhythms -- 2.2 The Influence of Microbiota on Host Rhythms and Metabolism -- 2.3 Perspectives and Challenges -- References -- Disease Implications of the Circadian Clocks and Microbiota Interface -- 1 Circadian Rhythms -- 2 Circadian Disruption.; 3 Implications of Circadian Disruption and the Microbiota.