Abstract
The self-organization of metabolic processes, such as the spontaneous dissipative formation of macromolecular structures, the functional coordination between multienzymatic complexes, and the emergence of molecular rhythms, is one of the most relevant topics in the post-genomic era. Herein, I analyze some aspects of self-organization in metabolic processes utilizing information theory to quantifying biomolecular information flows in bits, an approach that enables the visualization of emergent effective connectivity structures. Specifically, I determined the emergent functional integrative processes arising from irreversible enzymatic steps in yeast glycolysis, and in the systemic metabolic structure. Experimental observations and numerical studies with dissipative metabolic networks have shown that enzymatic activity can spontaneously self-organize leading to the emergence of a systemic metabolic structure, characterized by a set of different enzymatic reactions always locked into active states, i.e., the metabolic core, while the remaining catalytic processes are intermittently active. This global metabolic structure was verified in Escherichia coli, Helicobacter pylori, and Saccharomyces cerevisiae, and it seems to be a common key feature for all cells. The observed effective connectivity in both the irreversible enzymatic steps of yeast glycolysis and the systemic metabolic structure is highly dynamic and characterized by significant variations of biomolecular causality flows. These effective connectivity flows reflect the integration of catalytic processes within multienzymatic systems, and their functional coordination. The resulting functional integrative structures appear to be fundamental motifs in the dissipative self-organization and self-regulation of cellular metabolism.
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References
Ainscow EK, Mirsham S, Tang T, Ashford MLJ, Rutter GA (2002) Dynamic imaging of free cytosolic ATP concentration during fuel sensing by rat hypothalamic neurones: evidence for ATP independent control of ATP-sensitive K+ channels. J Physiol 544:429–45
Allegrini P, Buiatti M, Grigolini P, West BJ (1988) Fractal brownian motion as non stationary process: an alternative paradigm for DNA sequences. Phys Rev E 57:4558–62
Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabási AL (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427:839–43
Almaas E, Oltvai ZN, Barabasi AL (2005) The activity reaction core and plasticity of metabolic networks. PLoS Comput Biol 1(7):e68:0557–563
Almaas E (2007) Biological impacts and context of network theory. J Exp Biol 210:1548–58
Aon MA, Cortassa S (1997) Dynamic biological organization. Fundamentals as applied to cellular systems. Chapman & Hall, London, UK
Aon MA, Cortassa S, Lloyd D (2000) Chaotic dynamics and fractal space in biochemistry: simplicity underlies complexity. Cell Biol Int 24:581–87
Aon MA, Cortassa S, O'Rourke B (2004) Percolation and criticality in a mitochondrial network. Proc Natl Acad Sci USA 101:4447–52
Aon MA, Cortassa S, O’Rourke B (2006) The fundamental organization of cardiac mitochondria as a network of coupled oscillators. Biophys J 91:4317–27
Aon MA, Roussel MR, Cortassa S, O’Rourke B, Murray DB et al (2008) The scale-free dynamics of eukaryotic cells. PLoS One 3(e3624):1–12
Asano Y, Nagasaki A, Uyeda TQP (2008) Correlated waves of actin filaments and PIP3 in Dictyostelium cells. Cell Mot Cytosk 65:923–34
Audit B, Vaillant C, Arné A, D’Aubenton-Caraf Y, Thermes C (2004) Wavelet analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences. J Biol Phys 30:33–81
Barril EF, Potter AR (1968) Systematic oscillations of amino acid transport in liver from rats adapted to controlled feeding schedules. J Nutrition 95:228–37
Bastiaens P, Caudron M, Niethammer P, Karsenti E (2006) Gradients in the self-organization of the mitotic spindle. Trends Cell Biol 16(3):125–34
Bernardinelli Y, Magistretti PJ, Chatton JY (2004) Astrocytes generate Na+−mediated metabolic waves. Proc Natl Acad Sci USA 101:14937–42
Berridge MJ, Galione A (1988) Cytosolic calcium oscillators. FASEB J 2:3074–82
Bertschinger N, Natschlager T (2004) Real-time computation at the edge of Chaos in recurrent neural networks. Neural Comput 16:1413–36
Bobik TA (2006) Polyhedral organelles compartmenting bacterial metabolic processes. Appl Microbiol Biotechnol 70:517–25
Boiteux A, Goldbeter A, Hess B (1975) Control of oscillating glycolysis of yeast by stochastic, periodic, and steady source of substrate: a model and experimental study. Proc Natl Acad Sci USA 72:3829–33
Brodsky V, Boikov PY, Nechaeva NV, Yurovitsky YG, Novikova TE et al (1992) The rhythm of protein synthesis does not depend on oscillations of ATP level. J Cell Sci 103:363–70
Brodsky VY (2006) Direct cell-cell communication: a new approach derived from recent data on the nature and self-organisation of ultradian (circahoralian) intracellular rhythms. Biol Rev Camb Philos Soc 81:143–62
Cadena-Nava R, Comas-Garcia M, Garmann R, Rao ALN, Knobler C et al (2012) Self-assembly of viral capsid protein and RNA molecules of different sizes: requirement for a specific high protein/RNA mass ratio. J Virol 86(6):3318–26
Campanella ME, Chu H, Wandersee NJ, Peters LL, Mohandas N et al (2008) Characterization of glycolytic enzyme interactions with murine erythrocyte membranes in wild-type and membrane protein knockout mice. Blood 112(9):3900–6
Cascante M, Centelles JJ, Agius L (2000) Use of alpha-toxin from Staphylococcus aureus to test for channelling of intermediates of glycolysis between glucokinase and aldolase in hepatocytes. Biochem J 352(3):899–905
Cech T (2000) Structural biology. The ribosome is a ribozyme. Science 289(5481):878–9
Ceschini S, Lupidi G, Coletta M, Pon CL, Fioretti E et al (2000) Multimeric self-assembly equilibria involving the histone-like protein H-NS. A thermodynamic study. J Biol Chem 14(2):729–34
Chabot JR, Pedraza JM, Luitel P, van Oudenaarden A (2007) A Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature 450:1249–52
Chance B, Hess B, Betz A (1964) DPNH oscillations in a cell-free extract of S. carlsbergensis. Biochem Biophys Res Commun 16:182–7
Chance B, Pye EK, Ghosh AD, Hess B (1973) Biological and biochemical oscillations. Academic, New York, NY
Chandrashekaran MK (2005) Time in the living world. Universities Press, Hyderabad, India
Chiam HK, Rajagopal G (2007) Oscillations in intracellular signaling cascades. Phys Rev E 75:061901
Clarke FM, Masters CJ (1975) On the association of glycolytic enzymes with structural proteins of skeletal muscle. Biochim Biophys Acta 381:37–46
Clegg JS, Jackson SA (1990) Glucose metabolism and the channelling of glycolytic intermediates in permeabilized L-929 cells. Arch Biochem Biophys 278:452–60
Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, Lehnik-Habrink M, Hammer E, Völker U, Stülke J (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 8(6):1350–60
Connor KM, Gracey AY (2011) Circadian cycles are the dominant transcriptional rhythm in the intertidal mussel Mytilus californianus. Proc Natl Acad Sci 108:16110–5
Cortassa S, Aon MA, Westerhoff HV (1991) Linear non equilibrium thermodynamics describes the dynamics of an autocatalytic system. Biophys J 60:794–803
Cortassa S, Aon MA (1994) Spatio-temporal regulation of glycolysis and oxidative phosphorylation in vivo in tumor and yeast cells. Cell Biol Int 18(7):687–713
Cover T, Thomas J (1991) Elements of information theory. John Wiley & Sons, Inc.
Dano S, Sorensen P, Hynne F (1999) Sustained oscillations in living cells. Nature 402:320–2
De Forest M, Wheeler CJ (1999) Coherent oscillations in membrane potential synchronize impulse bursts in central olfactory neurons of the crayfish. J Neurophysiol 81:1231–41
Dekhuijzen A, Bagust J (1996) Analysis of neural bursting: nonrhythmic and rhythmic activity in isolated spinal cord. J Neurosci Methods 67:141–7
De la Fuente IM, Martínez L, Veguillas J (1995) Dynamic behavior in glycolytic oscillations with phase shifts. Biosystems 35:1–13
De la Fuente IM, Martínez L, Veguillas J (1996a) Intermittency route to Chaos in a biochemical system. Biosystems 39:87–92
De la Fuente IM, Martínez L, Veguillas J, Aguirregabiria JM (1996b) Quasiperiodicity route to Chaos in a biochemical system. Biophys J 71:2375–79
De la Fuente IM, Martínez L, Veguillas J, Aguirregabiria JM (1998a) Coexistence of multiple periodic and chaotic regimes in biochemical oscillations. Acta Biotheor 46:37–51
De la Fuente IM, Martinez L, Aguirregabiria JM, Veguillas J (1998b) R/S analysis in strange attractors. Fractals 6(2):95–100
De la Fuente IM, Martınez L, Benitez N, Veguillas J, Aguirregabiria JM (1998c) Persistent behavior in a phase-shift sequence of periodical biochemical oscillations. Bull Math Biol 60:689–702
De La Fuente IM, Benítez N, Santamaría A, Veguillas J, Aguirregabiria JM (1999a) Persistence in metabolic nets. Bull Mathemat Biol 61:573–95
De la Fuente IM (1999b) Diversity of temporal self-organized behaviors in a biochemical system. Biosystems 50:83–97
De la Fuente IM, Martínez L, Aguirregabiria JM, Veguillas J, Iriarte M (1999c) Long-range correlations in the phase-shifts of numerical simulations of biochemical oscillations and in experimental cardiac rhythms. J Biol Syst 7(2):113–30
De la Fuente IM, Pérez-Samartín A, Martínez L, García MA, Vera-López A (2006) Long-range correlations in rabbit brain neural activity. Ann Biomed Eng 34:295–9
De La Fuente IM, Martínez L, Pérez-Samartín AL, Ormaetxea L, Amezaga C et al (2008) Global Self-organization of the cellular metabolic structure. PLoS One 3:e3100
De La Fuente IM, Vadillo F, Pérez-Pinilla M-B, Vera-López A, Veguillas J (2009) The number of catalytic elements is crucial for the emergence of metabolic cores. PlosOne 4:e7510:1–e7510:11
De la Fuente IM (2010) Quantitative analysis of cellular metabolic dissipative. Self-organized structures. Int J Mol Sci 11(9):3540–99
De La Fuente IM, Vadillo F, Pérez-Samartín AL, Pérez-Pinilla M-B, Bidaurrazaga J et al (2010) Global self-regulations of the cellular metabolic structure. PlosOne 5:e9484:1–e9484:15
De la Fuente IM, Cortes J, Perez-Pinilla M, Ruiz-Rodriguez V, Veguillas J (2011) The metabolic core and catalytic switches are fundamental elements in the self-regulation of the systemic metabolic structure of cells. PLoS One 6:e27224
De la Fuente IM, Cortes JM (2012) Quantitative analysis of the effective functional structure in yeast glycolysis. PLoS One 7(2):e30162
De la Fuente IM, Cortes JM, Pelta D, Veguillas J (2013) Attractor metabolic networks. PLoS One 8:e58284
Dunlap JC, Loros JJ, DeCoursey P (2004) Chronobiology: biological timekeeping. Sinauer Associates, Sunderland, MA
Duysens L, Amesz J (1957) Fluorescence espectrophotometry of reduced phosphopyridine nucleotide in intact cells in the near-ultraviolet and visible region. Biochem Biophys Acta 24:19–26
Ebeling W, et al (1986) Selforganization by non-linear irreversible processes. In: Ebeling, W, Ulbricht H (eds) Thermodynamic aspects of selforganization. Springer, Berlin
Eke A, Herman P, Kocsis L, Kozak LR (2002) Fractal characterization of complexity in temporal physiological signals. Physiol Meas 23:R1–R38
Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS (2010) Short N-terminal sequences package proteins into bacterial microcompartments. Proc Natl Acad Sci USA 107:7509–14
Fuentes JM, Pascual MR, Salido G, Soler JA (1994) Madrid oscillations in rat liver cytosolic enzyme activities of the urea cycle. Arch Physiol Biochem 102(5):237–41
Gancedo C, Serrano R (1989) The yeasts. In: AH Rose, Harrison JS (eds) The yeasts. Academic, London, UK.
Galas L, Garnier M, Lamacz M (2000) Calcium waves in frog melanotrophs are generated by intracellular inactivation of TTX-sensitive membrane Na_ channel. Mol Cell Endocrinol 170:197–209
Garmendia-Torres C, Goldbeter A, Jacquet M (2007) Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation. Curr Biol 17:1044–49
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M et al (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–7
Getty L, Panteleon AE, Mittelman SD, Dea MK, Bergman RN (2000) Rapid oscillations in omental lipolysis are independent of changing insulin levels in vivo. J Clin Invest 106:421–30
Getty-Kaushik L, Richard AM, Corkey BE (2005) Free fatty acid regulation of glucose-dependent intrinsic oscillatory lipolysis in perifused isolated rat adipocytes. Diabetes 54(3):629–37
Glick BS (2007) Let there be order. Nat Cell Biol 9:130–2
Goldberger AL, Amaral LA, Hausdorff JM, Ivanov PCH, Peng CK, Stanley HE (2002) Fractal dynamics in physiology: alterations with disease and aging. Proc Natl Acad Sci USA 99:2466–72
Goldbeter A, Lefever R (1972) Dissipative structures for an allosteric model. Biophys J 12(10):1302–1315
Goldbeter A (1973) Patterns of spatiotemporal organization in an allosteric enzyme model. Proc Natl Acad Sci USA 70:3255–59
Goldbeter A (2002) Computational approaches to cellular rhythms. Nature 420:238–45
Goldbeter A (2007) Biological rhythms as temporal dissipative structures. Adv Chem Phys 135:253–95
Graham JW, Williams TC, Morgan M, Fernie AR, Ratcliffe RG et al (2007) Glycolytic enzymes associate dynamically with mitochondria in response to respiratory demand and support substrate channeling. Plant Cell 19(11):3723–38
Guthrie PB, Knappenberger J, Segal M, Bennett MVL, Charles AC et al (1999) ATP released from astrocytes mediates glial calcium waves. J Neurosci 19:520–8
Halley JD, Winkler DA (2008) Consistent concepts of self-organization and self-assembly. Complexity 14(2):10–17
Hans MA, Heinzle E, Wittmann C (2003) Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae. Biotechnol Bioeng 82(2):143–151
Hartig K, Beck E (2005) Endogenous cytokinin oscillations control cell cycle progression of tobacco BY-2 cells. Plant Biol 7(1):33–40
Haviv L, Brill-Karniely Y, Mahaffy R, Backouche F, Ben-Shaul A et al (2006) Reconstitution of the transition from lamellipodium to filopodium in a membrane-free system. Proc Natl Acad Sci USA 103:4906–11
He C, Hus JC, Sun LJ, Zhou P, Norman DP et al (2005) A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada. Mol Cell 20:117–29
Heinisch JJ, Boles E, Timpel C (1996) A yeast phosphofructokinase insensitive to the allosteric activator fructose-2,6-bisphosphate. J Biol Chem 271:15928–33
Hildebrandt G (1982) The time structure of adaptive processes. Georg Thieme Verlag, Stuttgart, Germany
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L et al (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–3
Holz GG, Emma Heart E, Leech CA (2008) Synchronizing Ca2+ and cAMP oscillations in pancreatic beta cells: a role for glucose metabolism and GLP-1 receptors? Am J Physiol Cell Physiol 294:c4–c6
Huber F, Käs J (2011) Self-regulative organization of the cytoskeleton. Cytoskeleton 68(5):259–65
Hungerbuehler AK, Philippsen P, Gladfelter AS (2007) Limited functional redundancy and oscillation of cyclins in multinucleated Ashbya gossypii fungal cells. Eukaryot Cell 6(3):473–86
Ishii K, Hirose K, Iino M (2006) Ca2+ shuttling between endoplasmic reticulum and mitochondria underlying Ca2+ oscillations. EMBO 7:390–6
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M et al (2001) Comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569–74
Ishikawa M, Tsuchiya D, Oyama T, Tsunaka Y, Morikawa K et al (2004) Structural basis for channelling mechanism of a fatty acid bold beta-oxidation multienzyme complex. EMBO J 23:2745–54
Jorgensen K, Rasmussen AV, Morant M, Nielsen AH, Bjarnholt N et al (2005) Metabolon formation and metabolic channeling in the biosynthesis of plant natural products. Curr Opin Plant Biol 8:280–91
Jovanović S, Jovanović A, Crawford MR (2007) M-ldh serves as a regulatory subunit of the cytosolic substrate-channelling complex in vivo. J Mol Biol 371:349–61
Jules M, Francois J, Parrou JL (2005) Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose. FEBS J 272:1490–1500
Karsenti E (2008) Self-organization in cell biology: a brief history. Nat Rev Mol Cell Biol 9(3):255–62
Kauffman S, Johnsen S (1991) Coevolution to the edge of chaos: coupled fitness landscapes, poised states, and coevolutionary avalanches. J Theor Biol 149:467–505
Kauffman S (1993) Origins of order: self-organization and selection in evolution. Oxford University Press, Oxford
Kazachenko VN, Astashev ME, Grinevic AA (2007) Multifractal analysis of K+ channel activity. Biochemistry (Moscow) 2:169–75
Kindzelskii AL, Zhou MJ, Haugland PR, Boxer AL, Petty RH (1998) Oscillatory pericellular proteolysis and oxidant deposition during neutrophil locomotion. Biophys J 74:90–7
Klevecz RR, Murray DB (2001) Genome wide oscillations in expression—wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype. Mol Biol Rep 28:73–82
Klevecz RR, Bolen J, Forrest G, Murray DB (2004) A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci 101(5):1200–05
Klimontovich YL (1999) Entropy and information of open systems. Phys-Uspekhi 42:375–84
Kushner DJ (1969) Self-assembly of biological structures. Bacteriol Rev 33:302–45
Lange G, Mandelkow EM, Jagla A, Mandelklow E (2004) Tubulin oligomers and microtubule oscillations antagonistic role of microtubule stabilizers and destabilizers. FEBS 178:61–9
Lehman JJ, Kelly DP (2002) Transcriptional activation of energy metabolic switches in the developing and hypertrophied heart. Clin Exp Pharmacol Physiol 29:339–45
Levine AJ, Puzio-Kuter AM (2010) The control of the metabolic switch in cancers by oncogenes and tumor suppressor genes. Science 330:1340–44
Lee CF (2008) Self-assembly of protein amyloids: a competition between amorphous and ordered aggregation. Phys Rev E 80(3):1–5
Lilley D (2005) Structure, folding and mechanisms of ribozymes. Curr Opin Struct Biol 15(3):313–23
Lim HN, van Oudenaarden A (2007) A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet 39:269–75
Lloyd D, Eshantha L, Salgado J, Turner MP, Murray DB (2002) Respiratory oscillations in yeast: clock-driven mitochondrial cycles of energization. FEBS Lett 519(1–3):41–4
Lloyd D (2005) Systems dynamics of biology. J Appl Biomed 3:1.12
Lloyd D, Murray DB (2005) Ultradian metronome: timekeeper for orchestration of cellular coherence. Trends Biochem Sci 30(7):373–7
Lloyd D, Murray DB (2006) The temporal architecture of eukaryotic growth. FEBS Lett 580:2830–35
Lloyd D, Murray DB (2007) Redox rhythmicity at the core of temporal coherence. Bioessays 29:465–73
Lloyd D, Douglas B, Murray DB (2006) The temporal architecture of eukaryotic growth. FEBS Lett 580:2830–5
Loose M, Fischer-Friedrich E, Ries J, Kruse K, Schwille P (2008) Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science 320(5877):789–92
Lunn EJ (2007) Compartmentation in plant metabolism. J Exp Bot 58:35–47
Mahasweta D, Gebber GL, Barman SM, Lewis CD (2003) Fractal properties of sympathetic nerve discharge. J Neurophysiol 89:833–40
Mair T, Warnke C, Muller SC (2001) Spatio-temporal dynamics in glycolysis. Faraday Discuss 120:249–59
Malaisse WJ, Zhang Y, Jijakli H, Courtois P, Sener A (2004) Enzyme-to-enzyme channelling in the early steps of glycolysis in rat pancreatic islets. Int J Biochem Cell Biol 36(8):1510–20
Madsen MF, Danø S, Sørensen PG (2005) On the mechanisms of glycolytic oscillations in yeast. FEBS J 272:2648–60
Markus M, Plesser T, Boiteux A, Hess B, Malcovati M (1980) Rate law of pyruvate kinase type I from Escherichia coli. Biochem J 189:421–33
Markus M, Kuschmitz D, Hess B (1984) Chaotic dynamics in yeast glycolysis under periodic substrate input flux. FEBS 172:235–38
Markus M, Kuschmitz D, Hess B (1985a) Properties of strange attractors in yeast glycolysis. Biophys Chem 22:95–105
Markus M, Muller S, Hess B (1985b) Observation of entrainment quasiperiodicity and chaos in glycolyzing yeast extracts under periodic glucose input. Ber Bunsen-Ges Phys Chem 89:651–54
Marquez S, Crespo P, Carlini V, Garbarino-Pico E, Baler R et al (2004) The metabolism of phospholipids oscillates rhythmically in cultures of fibroblasts and is regulated by the clock protein PERIOD 1. FASEB J 18:519–21
Mitchison TJ (1992) Self-organization of polymer-motor systems in the cytoskeleton. Philos Trans R Soc Lond B Biol Sci 336:99–106
Milani M, Pesce A, Bolognesi M, Bocedi A, Ascenzi P (2003) Substrate channeling: molecular bases. Biochem Mol Biol 31:228–33
Miller P, Zhabotinsky AM, Lisman JE, Wang X-J (2005) The stability of a stochastic CaMKII switch: dependence on the number of enzyme molecules and protein turnover. PLoS Biol 3:e107
Misteli T (2009) Self-organization in the genome. PNAS 106(17):6885–6
Møller AC, Hauser MJB, Olsen LF (1998) Oscillations in peroxidase-catalyzed reactions and their potential function in vivo. Biophys Chem 72:63–72
Monge C, Beraud N, Kuznetsov AV, Rostovtseva T, Sackett D (2008) Regulation of respiration in brain mitochondria and synaptosomes: restrictions of ADP diffusion in situ, roles of tubulin, and mitochondrial creatine kinase. Mol Cell Biochem 318:147–65
Monge C, Grichine A, Rostovtseva T, Sackett P, Saks VA (2009) Compartmentation of ATP in cardiomyocytes and mitochondria. Kinetic studies and direct measurements. Biophys J 96:241
Mowbray J, Moses V (1976) The tentative identification in Escherichia coli of a multienzyme complex with glycolytic activity. J Biochem 66:25–36
Murray D, Beckmann M, Kitano H (2007) Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci 104(7):2241–46
Nakahata Y, Grimaldi B, Sahar S, Hirayama J, Sassone-Corsi P (2007) Signaling to the circadian clock: plasticity by chromatin remodelling. Curr Opin Cell Biol 19:230–7
Negrutskii BS, Deutscher MP (1991) Channeling of aminoacyl tRNA for protein synthesis in vivo. Proc Natl Acad Sci USA 88:4991–5
Newman EA (2001) Propagation of intercellular calcium waves in retinal astrocytes and müller cells. J Neurosci 21:2215–23
Nicolis G, Prigogine I (1977) Self-organization in nonequilibrium systems. From dissipative structures to order through fluctuations. Wiley, New York
Oesch-Bartlomowicz B, Oesch F (2003) Cytochrome-P450 phosphorylation as a functional switch. Arch Biochem Biophys 409:228–34
Olsen LF, Degn H (1985) Chaos in biological systems. Q Rev Biophys 18:165–225
Olsen L, Andersen A, Lunding A, Brasen J, Poulsen A (2009) Regulation of glycolytic oscillations by mitochondrial and plasma membrane H+−ATPases. Biophys J 96:38503861
Oliva A, Rosebrock A, Ferrezuelo F, Pyne S, Chen H et al (2005) The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol 3:1239–60
Ovádi J, Srere PA (2000) Macromolecular compartmentation and channeling. Int Rev Cytol 192:255–80
Ovádi J, Saks V (2004) On the origin of the ideas of intracellular compartmentation and organized metabolic systems. Mol Cell Biochem 256–257(1–2):5–12
Pang CN, Krycer JR, Lek A, Wilkins MR (2008) Are protein complexes made of cores, modules and attachments? Proteomics 8(3):425–34
Pasini D, Malatesta M, Jung HR, Walfridsson J, Willer A et al (2010) Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res 38:4958–69
Perl A, Gergely P, Puskas F, Banki K (2002) Metabolic switches of T-cell activation and apoptosis. Antioxid Redox Signal 4:427–43
Petty HR, Worth RG, Kindzelskii AL (2000) Imaging sustained dissipative patterns in the metabolism of individual living cells. Phys Rev Lett 84:2754–57
Petty HR, Kindzelskii AL (2001) Dissipative metabolic patterns respond during neutrophil transmembrane signaling. Proc Natl Acad Sci USA 98:3145–49
Petty HR (2006) Spatiotemporal chemical dynamics in living cells: from information trafficking to cell physiology. Biosystems 83:217–24
Placantonakis DG, Welsh JP (2001) Two distinct oscillatory states determined by the NMDA receptor in rat inferior olive. J Physiol 534:123–40
Prigogine I, Mayné F, George C, De Haan M (1977) Microscopic theory of irreversible processes. Proc Nat Acad Sci USA 74:4152–56
Ramanujan VK, Biener G, Herman B (2006) Scaling behavior in mitochondrial redox fluctuations. Biophys J 90:L70–L72
Rengan R, Omann GM (1999) Regulation of oscillations in filamentous actin content in polymorphonuclear leukocytes stimulated with leukotriene B4 and platelet-activating factor. Biochem Biophys Res Commun 262:479–86
Romashko DN, Marban E, O’Rourke B (1998) Subcellular metabolic transients and mitochondrial redox waves in heart cells. Proc Natl Acad Sci USA 1998(95):1618–23
Rosenspire AJ, Kindzelskii AL, Petty H (2001) Pulsed DC electric fields couple to natural NAD(P)H oscillations in HT-1080 fibrosarcoma cells. J Cell Sci 114:1515–20
Roussel MR, Ivlev AA, Igamberdiev AU (2006) Oscillations of the internal CO2 concentration in tobacco leaves transferred to low CO2. J Plant Physiol 34:1188–96
Roussel MR, Lloyd D (2007) Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture. FEBS J 274:1011–18
Ruelle D, Takens F (1971) On the nature of turbulence. Commun Math Phys 20:167–72
Saks V, Dzeja P, Schlattner U, Vendelin M, Terzic A et al (2006) Cardiac system bioenergetics: metabolic basis of the Frank-Starling law. J Physiol 571:253–73
Saks VA, Monge C, Anmann T, Dzeja P (2007) Integrated and organized cellular energetic systems: Theories of cell energetics, compartmentation and metabolic channeling. In: Saks VA (ed) Molecular system bioenergetics. Energy for life. Wiley-VCH, Weinheim, Germany
Saks V, Monge C, Guzun R (2009) Philosophical basis and some historical aspects of systems biology: from hegel to noble—applications for bioenergetic research. Int J Mol Sci 10:1161–92
Sánchez-Armáss S, Sennoune SR, Maiti D, Ortega F, Martínez-Zaguila R (2006) Spectral imaging microscopy demonstrates cytoplasmic pH oscillations in glial cells. Am J Physiol Cell Physiol 290:C524–C538
Scemes E, Giaume C (2006) Astrocyte calcium waves: what they are and what they do. Glia 54:716–25
Schibler U, Sassone-Corsi PA (2002) Web of circadian pacemakers. Cell 111:919–22
Schibler U, Naef F (2005) Cellular oscillators: rhythmic gene expression and metabolism. Curr Opin Cell Biol 17:223–9
Shaul O, Mironov V, Burssens S, Van Montagu M, Inze D (1996) Two Arabidopsis cyclin promoters mediate distinctive transcriptional oscillation in synchronized tobacco BY-2 cells. Proc Natl Acad Sci 93(10):4868–72
Shankaran H, Ippolito DL, Chrisler WB, Resat H, Bollinger K et al (2009) Rapid and sustained nuclear–cytoplasmic ERK oscillations induced by epidermal growth factor. Mol Syst Biol 332:1–13
Shearer G, Lee JC, Koo JA, Kohl DH (2005) Quantitative estimation of channeling from early glycolytic intermediates to CO in intact Escherichia coli. FEBS J 272(13):3260–9
Schreiber T (2000) Measuring information transfer. Phys Rev Lett 85:461–64
Slaby O, Lebiedz D (2009) Oscillatory NAD(P)H waves and calcium oscillations in neutrophils? A modeling study of feasibility. Biophys J 96:417–28
Smrcinová M, Sørensen PG, Krempasky J, Ballo P (1998) Chaotic oscillations in a chloroplast system under constant illumination. Int J Bifurcat Chaos 8:2467–70
Sourjik V, Armitage JP (2010) Spatial organization in bacterial chemotaxis. EMBO J 29(16):2724–33
Stryer L (1995) Biochemistry. W.H. Freeman, New York
Sutter M, Boehringer D, Gutmann S, Günther S, Prangishvili D et al (2008) Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol 15:939–47
Talkington MW, Siuzdak G, Williamson JR (2005) An assembly landscape for the 30S ribosomal subunit. Nature 438:628–32
Tennessen JM, Baker KD, Lam G, Evans J, Thummel CS (2011) The Drosophila estrogen-related receptor directs a metabolic switch that supports developmental growth. Cell Metab 13:139–48
Termonia Y, Ross J (1981) Oscillations and control features in glycolysis: Numerical analysis of a comprehensive models. Proc Natl Acad Sci USA 78:29522956
Tian B, Nowak DE, Brasier AR (2005) A TNF-induced gene expression program under oscillatory NF-κB control. BMC Genom 6:137
Tonozuka H, Wang J, Mitsui K, Saito T, Hamada Y et al (2001) Analysis of the upstream regulatory region of the GTS1 gene required for its oscillatory expression. J Biochem 130:589–95
Tresset G (2009) The multiple faces of self-assembled lipidic systems. PMC Biophys 17 2(1):3
Tu BP, Kudlicki A, Rowicka M, McKnight SL (2005) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310:1152–58
Tyson J, Novak B, Odell MG, Chen K, Thron CD (1996) Chemical kinetic theory: understanding cell-cycle regulation. TIBS 21:89–96
Ueda T, Nakagaki T, Yamada T (1990) Dynamic organization of ATP and birefringent fibrils during free locomotion and galvanotaxis in the plasmodium of Physarum polycephalum. J Cell Biol 110:1097–02
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS et al (2000) A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403:623–27
Vanin AF, Ivanov VI (2008) Interaction of iron ions with oxygen or nitrogen monoxide in chromosomes triggers synchronous expression/suppression oscillations of compact gene groups (“genomewide oscillation”): Hypothesis. Nitric Oxide 18:147–52
Vasseur S, Tomasini R, Tournaire R, Iovanna JL (2010) Hypoxia induced tumor metabolic switch contributes to pancreatic cancer aggressiveness. Cancers 2:2138–52
Verkest A, Weinl C, Inzé D, De Veylder L, Schnittger A (2005) Switching the cell cycle. Kip-Related Proteins in Plant Cell Cycle Control Plant Physiol 139:1099–106
Vicker MG (2002) Eukaryotic cell locomotion depends on the propagation of self-organized reaction–diffusion waves and oscillations of actin filament assembly. Exp Cell Res 275:54–66
Viola E, Raushel M, Rendina R, Cleland W (1982) Substrate synergism and the kinetic mechanism of yeast hexokinase. Biochemistry 21:1295–302
Viswanathan GM, Buldyrev SV, Havlin S, Stanley HE (1997) Quantification of DNA patchiness using long-range correlation measures. Biophys J 72:866–75
Waingeh VF, Gustafson CD, Kozliak EI, Lowe SL, Knull HR, Thomasson KA (2006) Glycolytic enzyme interactions with yeast and skeletal muscle F-actin. Biophys J 90(4):1371–84
Whitesides GM, Grzybowski B (2002) Self-assembly at all scales. Science 295:2418–21
Wijnen H, Young MW (2006) Interplay of circadian clocks and metabolic rhythms. Annu Rev Genet 40:409–48
Wittmann C, Hans M, Van Winden AW, Ras C, Heijnen JJ (2005) Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae. Biotechnol Bioeng 89:839–47
Wolf J, Passarge J, Somsen OJG, Snoep JL, Heinrich R, Westerhof HV (2000) Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. Biophys J 78:1145–53
Woodford C, Zandstra PW (2012) Tissue engineering 2.0: guiding self-organization during pluripotent stem cell differentiation. Curr Opin Biotechnol 23:1–10
Xu SB, Li T, Deng ZY, Chong K, Xue Y et al (2008) Dynamic proteomic analysis reveals a switch between central carbon metabolism and alcoholic fermentation in rice filling grains. Plant Physiol 148:908–25
Yates FE (1993) Self-organizing systems. In: Boyd CAR, Noble D (eds) The logic of life. Oxford University Press, Oxford, UK
Yeates TO, Tsai Y, Tanaka S, Sawaya MR, Kerfeld CA (2007) Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells. Biochem Soc Trans 35:508–11
Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM (2008) Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 6:681–91
Zhang Y, Jijakli H, Courtois P, Sener A, Malaisse WJ (2005) Impaired enzyme-to-enzyme channelling between hexokinase isoenzyme(s) and phosphoglucoisomerase in rat pancreatic islets incubated at a low concentration of D-glucose. Cell Biochem Funct 23(1):15–21
Zhaojun XU, So-ichi Y, Kunio T (2004) Gts1p stabilizes oscillations in energy metabolism by activating the transcription of TPS1 encoding trehalose-6-phosphate synthase 1 in the yeast Saccharomyces cerevisiae. Biochem J 383:171–8
Zhou L, Aon MA, Almas T, Cortassa S, Winslow RL et al (2010) A reaction–diffusion model of ROS-induced ROS release in a mitochondrial network. PLoS Comput Biol 6(1):e1000657
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de la Fuente, I.M. (2014). Metabolic Dissipative Structures. In: Aon, M., Saks, V., Schlattner, U. (eds) Systems Biology of Metabolic and Signaling Networks. Springer Series in Biophysics, vol 16. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38505-6_8
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