The physics of bacterial decision making.
The choice that bacteria make between sporulation and competence when subjected to stress provides a prototypical example of collective cell fate determination that is stochastic on the individual cell level, yet predictable (deterministic) on the population level. This collective decision is performed by an elaborated gene network. Considerable effort has been devoted to simplify its complexity by taking physics approaches to untangle the basic functional modules that are integrated to form the complete network: (1) A stochastic switch whose transition probability is controlled by two order parameters-population density and internal/external stress. (2) An adaptable timer whose clock rate is normalized by the same two previous order parameters. (3) Sensing units which measure population density and external stress. (4) A communication module that exchanges information about the cells' internal stress levels. (5) An oscillating gate of the stochastic switch which is regulated by the timer. The unique circuit architecture of the gate allows special dynamics and noise management features. The gate opens a window of opportunity in time for competence transitions, during which the circuit generates oscillations that are translated into a chain of short intervals with high transition probability. In addition, the unique architecture of the gate allows filtering of external noise and robustness against variations in circuit parameters and internal noise. We illustrate that a physics approach can be very valuable in investigating the decision process and in identifying its general principles. We also show that both cell-cell variability and noise have important functional roles in the collectively controlled individual decisions.
Center for Theoretical Biological Physics, Rice University Houston, TX, USA ; Department of Biosciences, Rice University Houston, TX, USA ; School of Physics and Astronomy and The Sagol School of Neuroscience, Tel-Aviv University Tel-Aviv, Israel.
Eshel
E
Ben-Jacob
Center for Theoretical Biological Physics, Rice University Houston, TX, USA.
Mingyang
M
Lu
Department of Systems Biology, Harvard Medical School Boston, MA, USA.
Daniel
D
Schultz
Center for Theoretical Biological Physics, Rice University Houston, TX, USA ; Department of Biosciences, Rice University Houston, TX, USA ; Department of Physics and Astronomy, Rice University Houston, TX, USA ; Department of Chemistry, Rice University Houston, TX, USA.
Jose' N
JN
Onuchic
D000465:Algorithms; D018407:Bacterial Physiological Phenomena; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D008954:Models, Biological; D013171:Spores, Bacterial / Q000502:physiology
Bacillus subtilis; cell communication; cell fate determination; computational modeling; gene circuits; noise management; sporulation and competence