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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

Short term phage-bacterial dynamics and a tragedy of the commons between two phage types. Free bacterial densities are in gray, refuge bacterial densities in black, genetically modified (GM) phage densities in red, and wild phage densities in blue. The rate at which refuge bacteria are released into the free state is in green, affected by enzyme density (not shown). Panels (A) and (B) represent cultures infected with single phage types. (A): The wild phage type has little effect on bacterial densities because it does not cause release of refuge bacteria; it maintains high levels by feeding on free bacteria released from the refuge. (B): The GM phage produces an enzyme that releases refuge bacteria. At high phage densities, refuge bacteria are released and killed rapidly, bacterial densities drop, and phage densities follow. (C): A tragedy of the commons. Both phages are present, and in the short term, the overall phage and bacterial dynamics follow a similar pattern as when only the GM phage is present, with refuge bacteria depleted (as in B). The wild phage has a slightly higher burst than the GM phage (20 versus 17); although both phages start out equally abundant, the GM phage declines and is eventually lost if the run is continued further, the dynamics returning to the pattern in (A). Loss of the GM phage is the ‘tragedy,’ since the GM phage releases refuge bacteria. (D): As in (C), but the wild phage is given the lower burst size (17 versus 20) and it is progressively lost. There is no tragedy because GM phage is maintained. When the GM phage is lost (in C), there is an earlier recovery of bacterial densities and earlier return of the release rate to baseline than in (D). The scale of the vertical axis is log 10.
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Figure 1: Short term phage-bacterial dynamics and a tragedy of the commons between two phage types. Free bacterial densities are in gray, refuge bacterial densities in black, genetically modified (GM) phage densities in red, and wild phage densities in blue. The rate at which refuge bacteria are released into the free state is in green, affected by enzyme density (not shown). Panels (A) and (B) represent cultures infected with single phage types. (A): The wild phage type has little effect on bacterial densities because it does not cause release of refuge bacteria; it maintains high levels by feeding on free bacteria released from the refuge. (B): The GM phage produces an enzyme that releases refuge bacteria. At high phage densities, refuge bacteria are released and killed rapidly, bacterial densities drop, and phage densities follow. (C): A tragedy of the commons. Both phages are present, and in the short term, the overall phage and bacterial dynamics follow a similar pattern as when only the GM phage is present, with refuge bacteria depleted (as in B). The wild phage has a slightly higher burst than the GM phage (20 versus 17); although both phages start out equally abundant, the GM phage declines and is eventually lost if the run is continued further, the dynamics returning to the pattern in (A). Loss of the GM phage is the ‘tragedy,’ since the GM phage releases refuge bacteria. (D): As in (C), but the wild phage is given the lower burst size (17 versus 20) and it is progressively lost. There is no tragedy because GM phage is maintained. When the GM phage is lost (in C), there is an earlier recovery of bacterial densities and earlier return of the release rate to baseline than in (D). The scale of the vertical axis is log 10.

Mentions: Representative short term dynamics are illustrated in Figure 1 and do not require understanding the equations. The top two panels show outcomes for environments with single phages, each with identical parameters except for enzyme production. In each, phage densities start out low and increase in response to the abundance of hosts. In (A), the wild phage cannot infect the refuge population because they cannot free it, so phage and bacteria are both maintained at high density – the refuge population continually generates free bacteria on which the wild phage preys. This equilibrium continues indefinitely. In (B), the GM phage frees refuge bacteria and exposes them to attack; the total bacterial density declines several logs once the phage reach high density, and because hosts are no longer abundant, phage densities then decline as well. If continued longer, the bacteria would rebound, and the phage would again rise to suppress their numbers; this longer time frame is not necessarily relevant to phage treatment applications. Because the GM phage is able to destroy the refuge bacteria, its numbers briefly spike above those of the wild phage (in A), but then the paucity of hosts causes GM phage densities to fall below those of the wild phage. The green curves show the (log 10) rate at which refuge bacteria are being released into the free population.


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)

Short term phage-bacterial dynamics and a tragedy of the commons between two phage types. Free bacterial densities are in gray, refuge bacterial densities in black, genetically modified (GM) phage densities in red, and wild phage densities in blue. The rate at which refuge bacteria are released into the free state is in green, affected by enzyme density (not shown). Panels (A) and (B) represent cultures infected with single phage types. (A): The wild phage type has little effect on bacterial densities because it does not cause release of refuge bacteria; it maintains high levels by feeding on free bacteria released from the refuge. (B): The GM phage produces an enzyme that releases refuge bacteria. At high phage densities, refuge bacteria are released and killed rapidly, bacterial densities drop, and phage densities follow. (C): A tragedy of the commons. Both phages are present, and in the short term, the overall phage and bacterial dynamics follow a similar pattern as when only the GM phage is present, with refuge bacteria depleted (as in B). The wild phage has a slightly higher burst than the GM phage (20 versus 17); although both phages start out equally abundant, the GM phage declines and is eventually lost if the run is continued further, the dynamics returning to the pattern in (A). Loss of the GM phage is the ‘tragedy,’ since the GM phage releases refuge bacteria. (D): As in (C), but the wild phage is given the lower burst size (17 versus 20) and it is progressively lost. There is no tragedy because GM phage is maintained. When the GM phage is lost (in C), there is an earlier recovery of bacterial densities and earlier return of the release rate to baseline than in (D). The scale of the vertical axis is log 10.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Short term phage-bacterial dynamics and a tragedy of the commons between two phage types. Free bacterial densities are in gray, refuge bacterial densities in black, genetically modified (GM) phage densities in red, and wild phage densities in blue. The rate at which refuge bacteria are released into the free state is in green, affected by enzyme density (not shown). Panels (A) and (B) represent cultures infected with single phage types. (A): The wild phage type has little effect on bacterial densities because it does not cause release of refuge bacteria; it maintains high levels by feeding on free bacteria released from the refuge. (B): The GM phage produces an enzyme that releases refuge bacteria. At high phage densities, refuge bacteria are released and killed rapidly, bacterial densities drop, and phage densities follow. (C): A tragedy of the commons. Both phages are present, and in the short term, the overall phage and bacterial dynamics follow a similar pattern as when only the GM phage is present, with refuge bacteria depleted (as in B). The wild phage has a slightly higher burst than the GM phage (20 versus 17); although both phages start out equally abundant, the GM phage declines and is eventually lost if the run is continued further, the dynamics returning to the pattern in (A). Loss of the GM phage is the ‘tragedy,’ since the GM phage releases refuge bacteria. (D): As in (C), but the wild phage is given the lower burst size (17 versus 20) and it is progressively lost. There is no tragedy because GM phage is maintained. When the GM phage is lost (in C), there is an earlier recovery of bacterial densities and earlier return of the release rate to baseline than in (D). The scale of the vertical axis is log 10.
Mentions: Representative short term dynamics are illustrated in Figure 1 and do not require understanding the equations. The top two panels show outcomes for environments with single phages, each with identical parameters except for enzyme production. In each, phage densities start out low and increase in response to the abundance of hosts. In (A), the wild phage cannot infect the refuge population because they cannot free it, so phage and bacteria are both maintained at high density – the refuge population continually generates free bacteria on which the wild phage preys. This equilibrium continues indefinitely. In (B), the GM phage frees refuge bacteria and exposes them to attack; the total bacterial density declines several logs once the phage reach high density, and because hosts are no longer abundant, phage densities then decline as well. If continued longer, the bacteria would rebound, and the phage would again rise to suppress their numbers; this longer time frame is not necessarily relevant to phage treatment applications. Because the GM phage is able to destroy the refuge bacteria, its numbers briefly spike above those of the wild phage (in A), but then the paucity of hosts causes GM phage densities to fall below those of the wild phage. The green curves show the (log 10) rate at which refuge bacteria are being released into the free population.

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