Bacterial persisters and phenotypic switching Balaban_ Merrin

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Bacterial persisters and phenotypic
Balaban, Merrin, Chait, Kowalik, and Leibler, “Bacterial persistence as a phenotypic switch,” Science
    305:1622—1625 (2004).
Dhar and McKinney, “Microbial phenotypic heterogeneity and antibiotic resistance,” Current Opinion in
    Microbiology 10:30—38 (2007).

Microfabricated record grooves— Chlorine and fluorine-based gases can be used to etch grooves in a
                            silicon wafer template. Uncured PDMS (polydimethylsiloxane, a
                            transparent, gel-like elasto-polymer) poured onto the template and cured
                            can then be removed for use.

                               E. coli mutants—hipA7 and hipQ are high persistence mutants, of the so-
                               called wild-type strain K-12, studied previously in the context of
                               ampicillin and quinolones.

Persisters—a subpopulation of cells with epigenetic drug tolerance. Phenotypic switching between
 persister and sensitive types, often assumed to be stochastic, dynamically generates heterogeneity even
 in the absence of drug. Drug tolerance is correlated with quiescence, particularly in bacteria, but cancer
 literature also reports expanding persisters. See also Sharma et al from the Settleman Lab, “A
 chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations,” Cell 141:69—80

Selected Leibler results
                                             hipA7                         hipQ
Generated before antibiotic stress?          Apparently during             Apparently during log-phase
                                             stationary phase              proliferation
Distinguishable according to                 Yes, quiescent                Yes, slow proliferation (~4hr
proliferation before exposure to                                           doubling as opposed to 40 min)
antibiotic stress?
Phenotypic reversion upon antibiotic         Yes, re-sensitization &       Yes, faster proliferation after
withdrawal                                   proliferation within ~7hr     ~5hr

Stochastic timing of chemical reactions.
Dhar, 33. “Noise can be . . . generated by the
inherent stochasticity in biochemical
processes involved in gene expression
within an individual cell . . . . contribution of
noise to variation in gene expression tends to
be more significant when smaller numbers of molecules or genes with essential functions are involved.
This suggests . . . that stresses that globally depress the rates of gene transcription and translation,
including many antibiotics, might result in increased phenotypic heterogeneity in bacterial
populations. A role for stochastic processes in the persister switch has been proposed, but
experimental verification of this concept is still preliminary.”

   PIBS BP 219 Journal Club: Persisters and phenotypic switching. 2011 November 15. (1-2) 1

Phenotypic switching.
Dhar, 33—34. “Well studied examples of
bistability in bacteria include induction/repression
of the lactose operon in E. coli, the competence
switch in B. subtilis, and the lysis/lysogeny decision
in bacteriophage lambda. In these and other cases,
phenotypic switching is controlled by a positive
(or double-negative) feedback loop that is
triggered when the expression of a key regulatory factor passes a certain threshold value. . . . the
molecular basis of the persister switch is unknown . . . .”

See also Raj and van Oudenaarden, “Nature, nurture, or chance: Stochastic gene expression and its
consequences,” Cell 135:216—226 (2008).

1. Some authors propose that drug tolerance occurs by virtue of reduced proliferation. Underlying
    molecular mechanisms have not been fully elucidated. Suppose that reduced proliferation and drug
    tolerance were controlled at some level by separate molecular circuitry. Could you devise an
    alternative explanation for why it might be evolutionarily advantageous to turn these circuits on and
    off together?
2. When does interconversion between normal and persistent phenotypes confer a population-wide
    proliferation advantage? Consider normal cells, persister cells, and environmental hospitality.
Event                                              dP/dt               Parameters n          p      E
Birth                                              b n (E = = 1)       b              +1
Become persister                                                                      -1      +1
Become normal
Environment becomes hostile                                                                           -1
Environment becomes hospitable

3. Is the positive-feedback system with cooperativity from last week’s class a realistic, plausible
    mechanism for bistability? Consider monomer gene products, dimers, and promoter activation.
Event                                             dP/dt              Parameters M D               Pr
Monomer production                                                   kr, krA          +1
Monomer degradation                               r M
Dimerization                                      kDIMERIZE M2                        -2      +1
Dimer dissociation                                                   kUNDIMERIZE
Dimer binding to promoter                                                                           +1
Dimer dissociation from promoter
If you like, see also the Dhar paper for more complicated proposed mechanisms for persister phenotypic

   PIBS BP 219 Journal Club: Persisters and phenotypic switching. 2011 November 15. (1-2) 2

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