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Challenges in predicting the evolutionary maintenance of a phage transgene.

Schmerer M, Molineux IJ, Ally D, Tyerman J, Cecchini N, Bull JJ - J Biol Eng (2014)

Bottom Line: Consistent with the previous study, the dispersin phage was superior to unmodified phage at clearing short term biofilms grown in broth, shown here to be an effect attributable to free enzyme.There was little empirical support for the tragedy of the commons framework despite a strong theoretical foundation for its supposed relevance.Expressed from a different part of the genome, the transgene did behave as if intrinsically costly, but its maintenance did not benefit from spatially structured growth per se - violating the tragedy framework.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA.

ABSTRACT

Background: In prior work, a phage engineered with a biofilm-degrading enzyme (dispersin B) cleared artificial, short-term biofilms more fully than the phage lacking the enzyme. An unresolved question is whether the transgene will be lost or maintained during phage growth - its loss would limit the utility of the engineering. Broadly supported evolutionary theory suggests that transgenes will be lost through a 'tragedy of the commons' mechanism unless the ecology of growth in biofilms meets specific requirements. We test that theory here.

Results: Functional properties of the transgenic phage were identified. Consistent with the previous study, the dispersin phage was superior to unmodified phage at clearing short term biofilms grown in broth, shown here to be an effect attributable to free enzyme. However, the dispersin phage was only marginally better than control phages on short term biofilms in minimal media and was no better than control phages in clearing long term biofilms. There was little empirical support for the tragedy of the commons framework despite a strong theoretical foundation for its supposed relevance. The framework requires that the transgene imposes an intrinsic cost, yet the transgene was intrinsically neutral or beneficial when expressed from one part of the phage genome. Expressed from a different part of the genome, the transgene did behave as if intrinsically costly, but its maintenance did not benefit from spatially structured growth per se - violating the tragedy framework.

Conclusions: Overall, the transgene was beneficial under many conditions, but no insight to its maintenance was attributable to the established evolutionary framework. The failure likely resides in system details that would be used to parameterize the models. Our study cautions against naive applications of evolutionary theory to synthetic biology, even qualitatively.

No MeSH data available.


Related in: MedlinePlus

Phage titers in the effluent of long term biofilms (the same biofilms assayed in Figure 5). The horizontal axis gives the number of days of phage treatment. Although titers one day after phage addition show some scatter, all treatments are clustered near 107/mL by day 3. Red: T7dsp (T7trx+dsp 10B), black: T7+, blue: an equal mixture of T7+ and T7dsp, and gray: an equal mixture of T7v and T7dsp. Error bars of ± 1 std. err. are shown. Logs are to base 10.
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Figure 6: Phage titers in the effluent of long term biofilms (the same biofilms assayed in Figure 5). The horizontal axis gives the number of days of phage treatment. Although titers one day after phage addition show some scatter, all treatments are clustered near 107/mL by day 3. Red: T7dsp (T7trx+dsp 10B), black: T7+, blue: an equal mixture of T7+ and T7dsp, and gray: an equal mixture of T7v and T7dsp. Error bars of ± 1 std. err. are shown. Logs are to base 10.

Mentions: Phage titers were monitored daily in the outflow of the silicone tubing in which the long-term biofilm was growing. Regardless of phage identity, titers were maintained near 107/mL (Figure 6). Thus despite clearing of the biofilm by the phage as revealed by CV staining, a reservoir of sensitive cells must have persisted to allow phage maintenance. The fact that phage titers were maintained at the same level across 4 days suggests minimal bacterial evolution to resist phage killing. The maintenance of phage likely reflects residual bacterial ‘wall growth’ and other refuges that the phage could not access (as noted for glass chambers in [18]), a model further supported by consideration of the biofilm flow rate: a 5 mm length of tubing experiences 90 replacement volumes of media per hour, so a population of purely suspended cells could not have maintained itself against this flow.


Challenges in predicting the evolutionary maintenance of a phage transgene.

Schmerer M, Molineux IJ, Ally D, Tyerman J, Cecchini N, Bull JJ - J Biol Eng (2014)

Phage titers in the effluent of long term biofilms (the same biofilms assayed in Figure 5). The horizontal axis gives the number of days of phage treatment. Although titers one day after phage addition show some scatter, all treatments are clustered near 107/mL by day 3. Red: T7dsp (T7trx+dsp 10B), black: T7+, blue: an equal mixture of T7+ and T7dsp, and gray: an equal mixture of T7v and T7dsp. Error bars of ± 1 std. err. are shown. Logs are to base 10.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4128545&req=5

Figure 6: Phage titers in the effluent of long term biofilms (the same biofilms assayed in Figure 5). The horizontal axis gives the number of days of phage treatment. Although titers one day after phage addition show some scatter, all treatments are clustered near 107/mL by day 3. Red: T7dsp (T7trx+dsp 10B), black: T7+, blue: an equal mixture of T7+ and T7dsp, and gray: an equal mixture of T7v and T7dsp. Error bars of ± 1 std. err. are shown. Logs are to base 10.
Mentions: Phage titers were monitored daily in the outflow of the silicone tubing in which the long-term biofilm was growing. Regardless of phage identity, titers were maintained near 107/mL (Figure 6). Thus despite clearing of the biofilm by the phage as revealed by CV staining, a reservoir of sensitive cells must have persisted to allow phage maintenance. The fact that phage titers were maintained at the same level across 4 days suggests minimal bacterial evolution to resist phage killing. The maintenance of phage likely reflects residual bacterial ‘wall growth’ and other refuges that the phage could not access (as noted for glass chambers in [18]), a model further supported by consideration of the biofilm flow rate: a 5 mm length of tubing experiences 90 replacement volumes of media per hour, so a population of purely suspended cells could not have maintained itself against this flow.

Bottom Line: Consistent with the previous study, the dispersin phage was superior to unmodified phage at clearing short term biofilms grown in broth, shown here to be an effect attributable to free enzyme.There was little empirical support for the tragedy of the commons framework despite a strong theoretical foundation for its supposed relevance.Expressed from a different part of the genome, the transgene did behave as if intrinsically costly, but its maintenance did not benefit from spatially structured growth per se - violating the tragedy framework.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA.

ABSTRACT

Background: In prior work, a phage engineered with a biofilm-degrading enzyme (dispersin B) cleared artificial, short-term biofilms more fully than the phage lacking the enzyme. An unresolved question is whether the transgene will be lost or maintained during phage growth - its loss would limit the utility of the engineering. Broadly supported evolutionary theory suggests that transgenes will be lost through a 'tragedy of the commons' mechanism unless the ecology of growth in biofilms meets specific requirements. We test that theory here.

Results: Functional properties of the transgenic phage were identified. Consistent with the previous study, the dispersin phage was superior to unmodified phage at clearing short term biofilms grown in broth, shown here to be an effect attributable to free enzyme. However, the dispersin phage was only marginally better than control phages on short term biofilms in minimal media and was no better than control phages in clearing long term biofilms. There was little empirical support for the tragedy of the commons framework despite a strong theoretical foundation for its supposed relevance. The framework requires that the transgene imposes an intrinsic cost, yet the transgene was intrinsically neutral or beneficial when expressed from one part of the phage genome. Expressed from a different part of the genome, the transgene did behave as if intrinsically costly, but its maintenance did not benefit from spatially structured growth per se - violating the tragedy framework.

Conclusions: Overall, the transgene was beneficial under many conditions, but no insight to its maintenance was attributable to the established evolutionary framework. The failure likely resides in system details that would be used to parameterize the models. Our study cautions against naive applications of evolutionary theory to synthetic biology, even qualitatively.

No MeSH data available.


Related in: MedlinePlus