Metabolic cycles as an underlying basis of biological oscillations

The evolutionary origins of periodic phenomena in biology, such as the circadian cycle, the hibernation cycle and the sleep–wake cycle, remain a mystery. We discuss the concept of temporal compartmentalization of metabolism that takes place during such cycles, and suggest that cyclic changes in a cell's metabolic state might be a fundamental driving force for such biological oscillations.

[1]  M. Yanagisawa,et al.  Orexins: from neuropeptides to energy homeostasis and sleep/wake regulation , 2002, Journal of Molecular Medicine.

[2]  F. Hommes.  OSCILLATORY REDUCTIONS OF PYRIDINE NUCLEOTIDES DURING ANAEROBIC GLYCOLYSIS IN BREWERS' YEAST. , 1964, Archives of biochemistry and biophysics.

[3]  H. Erfle,et al.  High-throughput RNAi screening by time-lapse imaging of live human cells , 2006, Nature Methods.

[4]  R. Pepperkok,et al.  Observing proteins in their natural habitat: the living cell. , 2000, Trends in biochemical sciences.

[5]  M. Reuss,et al.  Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae , 2003, Yeast.

[6]  D. Sabatini,et al.  Microarrays of cells expressing defined cDNAs , 2001, Nature.

[7]  J. Lippincott-Schwartz,et al.  Development and Use of Fluorescent Protein Markers in Living Cells , 2003, Science.

[8]  H. Heller,et al.  Sleep and circadian rhythms in mammalian torpor. , 2004, Annual review of physiology.

[9]  C. Johnson.  Endogenous timekeepers in photosynthetic organisms. , 2001, Annual review of physiology.

[10]  C. Conrad,et al.  Automatic identification of subcellular phenotypes on human cell arrays. , 2004, Genome research.

[11]  Kai Huang,et al.  Boosting accuracy of automated classification of fluorescence microscope images for location proteomics , 2004, BMC Bioinformatics.

[12]  M. Yanagisawa,et al.  Sleep, feeding, and neuropeptides: roles of orexins and orexin receptors , 2002, Current Opinion in Neurobiology.

[13]  D. L. Taylor,et al.  High content screening applied to large-scale cell biology. , 2004, Trends in biotechnology.

[14]  Stefan Wiemann,et al.  High-content screening microscopy identifies novel proteins with a putative role in secretory membrane traffic. , 2004, Genome research.

[15]  F. van Breukelen,et al.  Invited review: molecular adaptations in mammalian hibernators: unique adaptations or generalized responses? , 2002, Journal of applied physiology.

[16]  A. Ghosh,et al.  Oscillations of glycolytic intermediates in yeast cells. , 1964, Biochemical and biophysical research communications.

[17]  A. Pramanik.  Ligand-receptor interactions in live cells by fluorescence correlation spectroscopy. , 2004, Current pharmaceutical biotechnology.

[18]  A. Poustka,et al.  A microscope‐based screening platform for large‐scale functional protein analysis in intact cells , 2003, FEBS letters.

[19]  A. Kudlicki,et al.  Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes , 2005, Science.

[20]  V. Centonze,et al.  Microscopic analysis of fluorescence resonance energy transfer (FRET). , 2004, Methods in molecular biology.

[21]  松尾 拓哉.  Control mechanism of the circadian clock for timing of cell division in vivo , 2004 .

[22]  Jon T. Willie,et al.  Narcolepsy in orexin Knockout Mice Molecular Genetics of Sleep Regulation , 1999, Cell.

[23]  Timothy A. Dahl,et al.  Quantitative Analysis of Liver Protein Expression During Hibernation in the Golden-mantled Ground Squirrel*S , 2004, Molecular & Cellular Proteomics.

[24]  James G McNally,et al.  FRAP analysis of binding: proper and fitting. , 2005, Trends in cell biology.

[25]  J. Takahashi,et al.  Mammalian circadian biology: elucidating genome-wide levels of temporal organization. , 2004, Annual review of genomics and human genetics.

[26]  Stefan Wiemann,et al.  Illuminating the human genome , 2001, Histochemistry and Cell Biology.

[27]  A. Ghosh,et al.  DAMPED SINUSOIDAL OSCILLATIONS OF CYTOPLASMIC REDUCED PYRIDINE NUCLEOTIDE IN YEAST CELLS. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Sandra L Martin,et al.  Mammalian hibernation: cellular and molecular responses to depressed metabolism and low temperature. , 2003, Physiological reviews.

[29]  S. Kay,et al.  Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. , 2000, Science.

[30]  Peer Bork,et al.  Towards Cellular Systems in 4D , 2005, Cell.

[31]  F. Fleury-Olela,et al.  Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus. , 2000, Genes & development.

[32]  Takeharu Nagai,et al.  Engineering fluorescent proteins. , 2005, Advances in biochemical engineering/biotechnology.

[33]  A. Coulson,et al.  Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans , 2005, Nature.

[34]  Felix Naef,et al.  Circadian Gene Expression in Individual Fibroblasts Cell-Autonomous and Self-Sustained Oscillators Pass Time to Daughter Cells , 2004, Cell.

[35]  F. Geiser,et al.  Metabolic rate and body temperature reduction during hibernation and daily torpor. , 2004, Annual review of physiology.

[36]  Atsushi Miyawaki,et al.  Innovations in the Imaging of Brain Functions using Fluorescent Proteins , 2005, Neuron.

[37]  C. Woldringh,et al.  Effects of different carbon fluxes on G1 phase duration, cyclin expression, and reserve carbohydrate metabolism in Saccharomyces cerevisiae , 1997, Journal of bacteriology.

[38]  H. Kuriyama,et al.  Oscillatory metabolism of Saccharomyces cerevisiae in continuous culture. , 1992, FEMS microbiology letters.

[39]  Emmanuel Mignot,et al.  The Sleep Disorder Canine Narcolepsy Is Caused by a Mutation in the Hypocretin (Orexin) Receptor 2 Gene , 1999, Cell.

[40]  B. Schoener,et al.  CONTROLOF THE WAVEFORM OFOSCILLATIONS OF THE REDUCED PYRIDINENUCLEOTIDELEVEL IN A CELL-FREEEXTRACT , 1964 .

[41]  K. Onai,et al.  Mutation of the cys-9 gene, which encodes thioredoxin reductase, affects the circadian conidiation rhythm in Neurospora crassa. , 1997, Genetics.

[42]  S. McKnight,et al.  NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: genotype and sex interactions. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[43]  M. Ikeda,et al.  Brain oxidation is an initial process in sleep induction , 2005, Neuroscience.

[44]  S. Carr,et al.  Orexins and Orexin Receptors: A Family of Hypothalamic Neuropeptides and G Protein-Coupled Receptors that Regulate Feeding Behavior , 1998, Cell.

[45]  Michael J. McDonald,et al.  Microarray Analysis and Organization of Circadian Gene Expression in Drosophila , 2001, Cell.

[46]  D. Murray,et al.  A genomewide oscillation in transcription gates DNA replication and cell cycle. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[47]  T. Kondo,et al.  Reconstitution of Circadian Oscillation of Cyanobacterial KaiC Phosphorylation in Vitro , 2005, Science.

[48]  T. Mitchison,et al.  Phenotypic screening of small molecule libraries by high throughput cell imaging. , 2003, Combinatorial chemistry & high throughput screening.

[49]  A. Pack,et al.  Glycogen in the brain of Drosophila melanogaster: diurnal rhythm and the effect of rest deprivation , 2003, Journal of neurochemistry.

[50]  O. Pourquié.  The Segmentation Clock: Converting Embryonic Time into Spatial Pattern , 2003, Science.

[51]  Susan S. Golden,et al.  Cyanobacterial circadian clocks — timing is everything , 2003, Nature Reviews Microbiology.

[52]  C. Carey,et al.  Reversible Depression of Oxygen Consumption in Isolated Liver Mitochondria during Hibernation , 1999, Physiological and Biochemical Zoology.

[53]  Kai Simons,et al.  Multicolour imaging of post-Golgi sorting and trafficking in live cells , 2001, Nature Cell Biology.

[54]  S. Inoué,et al.  Sleep as neuronal detoxification and restitution , 1995, Behavioural Brain Research.

[55]  Anne E Carpenter,et al.  A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen , 2006, Cell.

[56]  Adam Claridge‐Chang,et al.  Circadian Regulation of Gene Expression Systems in the Drosophila Head , 2001, Neuron.

[57]  R. Tsien.  Building and breeding molecules to spy on cells and tumors , 2005, FEBS letters.

[58]  Anne E Carpenter,et al.  Cell microarrays and RNA interference chip away at gene function , 2005, Nature Genetics.

[59]  George H Patterson,et al.  Selective photolabeling of proteins using photoactivatable GFP. , 2004, Methods.

[60]  B. Binder,et al.  Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[61]  Robert F Murphy,et al.  Automated interpretation of subcellular patterns from immunofluorescence microscopy. , 2004, Journal of immunological methods.

[62]  M. Rosbash,et al.  The Coevolution of Blue-Light Photoreception and Circadian Rhythms , 2003, Journal of Molecular Evolution.

[63]  Weizhong Li,et al.  Seasonally hibernating phenotype assessed through transcript screening. , 2005, Physiological genomics.

[64]  Lani F. Wu,et al.  Multidimensional Drug Profiling By Automated Microscopy , 2004, Science.

[65]  B. H. Miller,et al.  Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock , 2002, Cell.

[66]  A. Poustka,et al.  CDNAs for functional genomics and proteomics: the German Consortium. , 2003, Comptes rendus biologies.

[67]  Thomas D Pollard,et al.  Counting Cytokinesis Proteins Globally and Locally in Fission Yeast , 2005, Science.

[68]  P. Schwille,et al.  Fluorescence correlation spectroscopy with autofluorescent proteins. , 2005, Advances in biochemical engineering/biotechnology.

[69]  A. Pack,et al.  Brain Glycogen Decreases with Increased Periods of Wakefulness: Implications for Homeostatic Drive to Sleep , 2002, The Journal of Neuroscience.

[70]  S. Golden,et al.  Circadian Rhythms in Rapidly Dividing Cyanobacteria , 1997, Science.

[71]  George H Patterson,et al.  Photobleaching and photoactivation: following protein dynamics in living cells. , 2003, Nature cell biology.

[72]  Y Sakaki,et al.  Entrainment of the circadian clock in the liver by feeding. , 2001, Science.

[73]  Tan-Chi Huang,et al.  Circadian Rhythm of the Prokaryote Synechococcus sp. RF-1. , 1990, Plant physiology.

[74]  Tobias Meyer,et al.  Fluorescence imaging of signaling networks. , 2003, Trends in cell biology.

[75]  H. Meyenburg.  Energetics of the budding cycle of Saccharomyces cerevisiae during glucose limited aerobic growth , 2004, Archiv für Mikrobiologie.

[76]  David Lloyd,et al.  Ultradian metronome: timekeeper for orchestration of cellular coherence. , 2005, Trends in biochemical sciences.

[77]  Konstantin A Lukyanov,et al.  Fluorescent proteins as a toolkit for in vivo imaging. , 2005, Trends in biotechnology.

[78]  A. Mitsui,et al.  Strategy by which nitrogen-fixing unicellular cyanobacteria grow photoautotrophically , 1986, Nature.

[79]  J. Siegel.  Clues to the functions of mammalian sleep , 2005, Nature.

[80]  G. Tononi,et al.  Extensive and Divergent Effects of Sleep and Wakefulness on Brain Gene Expression , 2004, Neuron.

[81]  F. Wouters,et al.  Imaging biochemistry inside cells. , 2001, Trends in cell biology.

[82]  Jared Rutter,et al.  Regulation of Clock and NPAS2 DNA Binding by the Redox State of NAD Cofactors , 2001, Science.

[83]  K. Storey.  Mammalian hibernation. Transcriptional and translational controls. , 2003, Advances in experimental medicine and biology.

[84]  S. Fields,et al.  Protein analysis on a proteomic scale , 2003, Nature.

[85]  R A Blake,et al.  Cellular screening assays using fluorescence microscopy. , 2001, Current opinion in pharmacology.

[86]  S. McKnight,et al.  NPAS2: A Gas-Responsive Transcription Factor , 2002, Science.

[87]  J. Ellenberg,et al.  Automatic real‐time three‐dimensional cell tracking by fluorescence microscopy , 2004, Journal of microscopy.

[88]  H. Gainer,et al.  Suprachiasmatic nucleus: use of 14C-labeled deoxyglucose uptake as a functional marker. , 1977, Science.

[89]  Timothy J Mitchison,et al.  Small‐Molecule Screening and Profiling by Using Automated Microscopy , 2005, Chembiochem : a European journal of chemical biology.

[90]  Jared Rutter,et al.  Metabolism and the control of circadian rhythms. , 2002, Annual review of biochemistry.