Kinetic Memory Based on the Enzyme-Limited Competition

PLoS Computational Biology

Volumn 10, Issue 8, 2014, Pages

  Hatakeyama, Tetsuhiro S ^a   Kaneko, Kunihiko ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; CALMODULIN; CATALYSIS; DYNAMICAL SYSTEMS; ENZYMES;

CELL DIFFERENTIATION; CELLULAR FUNCTION; CELLULAR MEMORY; EXTERNAL STIMULUS; MODIFICATION REACTIONS; POST-TRANSLATIONAL MODIFICATIONS; RELAXATION PHASIS; SLOW RELAXATIONS; STABLE STATE; SYNAPTIC PLASTICITY;

KINETICS;

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; ELONGATION FACTOR 2 KINASE; ENZYME;

ARTICLE; BINDING AFFINITY; BIOLOGICAL FUNCTIONS; CATALYSIS; CELL FUNCTION; CELLULAR MEMORY; CONTROLLED STUDY; ENVIRONMENTAL EXPOSURE; ENZYME LIMITED COMPETITION; ENZYME MODIFICATION; ENZYME SUBSTRATE; ENZYMOLOGY; EPIGENETICS; KINETIC MEMORY; LONG TERM POTENTIATION; NERVE CELL PLASTICITY; PHASE TRANSITION; PROTEIN METHYLATION; PROTEIN MODIFICATION; RELAXATION TIME; BIOCHEMISTRY; BIOLOGICAL MODEL; KINETICS; PHYSIOLOGY;

BIOCHEMICAL PHENOMENA; CELL PHYSIOLOGICAL PHENOMENA; ENZYMES; KINETICS; MODELS, BIOLOGICAL;

EID: 84927976278     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003784     Document Type: Article

References (38)

1. Wolf DM, Fontaine-Bodin L, Bischofs I, Price G, Keasling J, et al. (2008) Memory in microbes: quantifying history-dependent behavior in a bacterium. PloS One 3: e1700.
2. Guan Q, Haroon S, Bravo DG, Will JL, Gasch AP, (2012) (2012) Cellular memory of acquired stress resistance in Saccharomyces cerevisiae. Genetics 192: 495–505.
3. Jennings HS. (1906) Behavior of the lower organisms. New Yor: The Colombia University press.
4. Bliss TV & Lomo T, (1973) Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path. J Physiol 232: 331–56.
5. Bliss TV & Gardner-Medwin AR, (1973) Long-lasting potentiation of synaptic transmission in the dentate area of the unanaesthetized rabbit following stimulation of the perforant path. J Physiol 232: 357–74.
6. Sweatt JD, (1999) Toward a Molecular Explanation for Long-Term Potentiation. Learn Mem 6: 399–416.
7. Lisman J, Schulman H, Cline H, (2002) (2002) The molecular basis of CaMKII function in synaptic and behavioural memory. Nat Rev Neurosci 3: 175–90.
8. Silva AJ, Kogan JH, Frankland PW, Kida S, (1998) (1998) CREB and memory. Annu Rev Neurosci 21: 127–48.
9. Sasagawa S, Ozaki Yi, Fujita K, Kuroda S, (2005) (2005) Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat Cell Biol 7: 365–73.
10. Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C, (2006) (2006) Transcriptional dynamics of the embryonic stem cell switch. PLoS Comp Biol 2: e123.
11. Crick F, (1984) Neurobiology: Memory and molecular turnover. Nature 312: 101–101.
12. Lisman JE, (1985) A mechanism for memory storage insensitive to molecular turnover: a bistable autophosphorylating kinase. Proc Natl Acad Sci USA 82: 3055–7.
13. Thomson M & Gunawardena J, (2009) Unlimited multistability in multisite phosphorylation systems. Nature 460: 274–7.
14. Dodd IB, Micheelsen MA, Sneppen K, Thon G, (2007) (2007) Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129: 813–22.
15. Lisman JE & Goldring MA, (1988) Feasibility of long-term storage of graded information by the Ca2+/calmodulin-dependent protein kinase molecules of the postsynaptic density. Proc Natl Acad Sci USA 85: 5320–4.
16. Zhabotinsky AM, (2000) Bistability in the Ca2+/calmodulin-dependent protein kinase-phosphatase system. Biophys J 79: 2211–21.
17. Lisman JE & Zhabotinsky AM, (2001) A Model of Synaptic Memory: A CaMKII/PP1 Switch that Potentiates Transmission by Organizing an AMPA Receptor Anchoring Assembly. Neuron 31: 191–201.
18. Bradshaw JM, Kubota Y, Meyer T, Schulman H, (2003) (2003) An ultrasensitive Ca2+/calmodulin-dependent protein kinase II-protein phosphatase 1 switch facilitates specificity in postsynaptic calcium signaling. Proc Natl Acad Sci USA 100: 10512–7.
19. De Koninck P & Schulman H, (1998) Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations. Science 279: 227–30.
20. Sanhueza M, Fernandez-Villalobos G, Stein IS, Kasumova G, Zhang P, et al. (2011) Role of the CaMKII/NMDA receptor complex in the maintenance of synaptic strength. J Neurosci 31: 9170–8.
21. van Zon JS, Lubensky DK, Altena PRH, ten Wolde PR, (2007) (2007) An allosteric model of circadian KaiC phosphorylation. Proc Natl Acad Sci USA 104: 7420–5.
22. Tseng R, Chang YG, Bravo I, Latham R, Chaudhary A, et al. (2014) Cooperative KaiA–KaiB–KaiC Interactions Affect KaiB/SasA Competition in the Circadian Clock of Cyanobacteria. J Mol Biol 426: 389–402.
23. Debenedetti PG & Frank HS, (2001) Supercooled liquids and the glass transition. Nature 410: 259–267.
24. Ritort F & Peter S, (2003) Glassy dynamics of kinetically constrained models. Adv Phys 52: 219–342.
25. Awazu A & Kaneko K, (2009) Ubiquitous “glassy” relaxation in catalytic reaction networks. Phys Rev E 80: 041931.
26. McCarrey JR & Riggs AD, (1986) Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes. Proc Natl Acad Sci USA 83: 679–83.
27. Cohen P, (2000) The regulation of protein function by multisite phosphorylation–a 25 year update. Trends Biochem Sci 25: 596–601.
28. Holmberg CI, Tran SE, Eriksson JE & Sistonen L, (2002) Multisite phosphorylation provides sophisticated regulation of transcription factors. Trends Biochem Sci 27: 619–627.
29. Markevich NI, Hoek JB & Kholodenko BN, (2004) Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biol 164: 353–359.
30. Asakura S & Honda H, (1984) Two-state model for bacterial chemoreceptor proteins. The role of multiple methylation. J Mol Biol 176: 349–67.
31. Tu Y, (2008) The nonequilibrium mechanism for ultrasensitivity in a biological switch: Sensing by Maxwell's demons. Proc Nat Acad Sci USA 105: 11737–11741.
32. Hatakeyama TS & Kaneko K, (2012) Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration. Proc Natl Acad Sci USA 109: 8109–14.
33. Hatakeyama TS & Kaneko K, (2014) Homeostasis of the period of post-translational biochemical oscillators. FEBS Lett 588: 2282–87.
34. Bito H, Deisseroth K, Tsien RW, (1996) (1996) CREB phosphorylation and dephosphorylation: a Ca2+ and stimulus duration-dependent switch for hippocampal gene expression. Cell 87: 1203–14.
35. Nakaoka Y, Tokui H, Gion Y, Inoue S, Oosawa F, (1982) (1982) Behavioral Adaptation of Paramecium caudatum to Environmental Temperature. Proc Japan Acad Ser B 58: 213–217.
36. Kimura KD, Miyawaki A, Matsumoto K, Mori I, (2004) (2004) The C. elegans thermosensory neuron AFD responds to warming. Curr Biol 14: 1291–5.
37. Saeki S, Yamamoto M, Iino Y, (2001) (2001) Plasticity of chemotaxis revealed by paired presentation of a chemoattractant and starvation in the nematode Caenorhabditis elegans. J Exp Biol 204: 1757–64.
38. Oda S, Tomioka M, Iino Y, (2011) (2011) Neuronal plasticity regulated by the insulin-like signaling pathway underlies salt chemotaxis learning in Caenorhabditis elegans. J Neurophysiol 106: 301–8.