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Literature DB >> 18971947

Design principles of biochemical oscillators.

Abstract

Cellular rhythms are generated by complex interactions among genes, proteins and metabolites. They are used to control every aspect of cell physiology, from signalling, motility and development to growth, division and death. We consider specific examples of oscillatory processes and discuss four general requirements for biochemical oscillations: negative feedback, time delay, sufficient 'nonlinearity' of the reaction kinetics and proper balancing of the timescales of opposing chemical reactions. Positive feedback is one mechanism to delay the negative-feedback signal. Biological oscillators can be classified according to the topology of the positive- and negative-feedback loops in the underlying regulatory mechanism.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2008 PMID： 18971947 PMCID： PMC2796343 DOI： 10.1038/nrm2530

Source DB: PubMed Journal: Nat Rev Mol Cell Biol ISSN： 1471-0072 Impact factor: 94.444

59 in total

Design principles of biochemical oscillators.

1. Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays.

2. Mechanism for oscillatory synthesis of cyclic AMP in Dictyostelium discoideum.

3. Control of cell-contact sites by cyclic AMP pulses in differentiating Dictyostelium cells.

4. Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation.

5. A plausible model for the digital response of p53 to DNA damage.

6. A principle for chemical multivibration.

7. Mathematics of cellular control processes. I. Negative feedback to one gene.

8. Cyclin: a protein specified by maternal mRNA in sea urchin eggs that is destroyed at each cleavage division.

9. An amplified sensitivity arising from covalent modification in biological systems.

10. A fast, robust and tunable synthetic gene oscillator.

1. Multisite phosphoregulation of Cdc25 activity refines the mitotic entrance and exit switches.

2. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle.

3. A multiphysics model of in vitro transcription coupling enzymatic reaction and precipitation formation.

4. Regulation of oscillation dynamics in biochemical systems with dual negative feedback loops.

5. Transcription factor oscillations induce differential gene expressions.

6. What is the core oscillator in the speract-activated pathway of the Strongylocentrotus purpuratus sperm flagellum?

7. Architecture-dependent robustness and bistability in a class of genetic circuits.

8. Costs and constraints from time-delayed feedback in small gene regulatory motifs.

Review 9. Clocks not winding down: unravelling circadian networks.

Review 10. A comparative analysis of synthetic genetic oscillators.