Correlations between Phage Life History Traits and Phage Particle Characteristics

<div><p>(A) Positive correlation between mortality rate and <i>ρ_pack, </i> the volumic density of the packaged DNA (Linear regression, <i>R²</i> = 0.67 and <i>p</i> = 0.001). <i>ρ_pack</i> has been calculated only for phages with a double-stranded DNA genome, because the volumes of single-strand DNA and double-strand RNA are different than the volume of double-stranded DNA. <i>ρ_pack</i> is calculated by dividing the volume of the genome by the internal volume of the capsid. </p> <p>(B) Negative correlation between mortality rate and the surfacic mass of the capsid, calculated by dividing the capsid molecular weight by capsid surface (linear regression, <i>R²</i> = 0.35 and <i>p</i> = 0.031). Because the surfacic mass is an estimation of the thickness of the capsid, it should be related to its strength. Some phages are not represented because data are not available, or in the case of M13, because it possesses a helical geometry, and thus the constraints on the capsid are very different than for icosahedral phages. </p> <p>(C) Negative correlation between the multiplication rate and the surfacic mass of the capsid (linear regression, <i>R²</i> = 0.46 and <i>p</i> = 0.011). </p> <p>(D) Positive correlation between the mortality rate and the multiplication rate. The log–log scale is for a better visualization of the results and does not modify the significance of the correlation. The line shows a linear regression characterized by <i>R²</i> = 0.73 and <i>p</i> < 0.0001. Each measure was repeated at least three times independently for the determination of the multiplication and mortality rates. </p></div

Observation of Virions by Electron Microscopy after 8 D of Incubation at 37 °C

<p>The table gives the relative variation in the proportion of broken virions, as measured by electron microscopy, of more than a hundred particles, as well as the variation in the number of viable phages measured by plating on a susceptible host. Both observations have been made on the same samples. For each type of phage, the proportion of broken virions is significantly higher after incubation, and the variation in broken-virion particles measured by electron microscopy is similar to the variation in the number of infectious phages.</p

Actual Mortality Rate against Predicted Decay Rate by a Model of Multiple Regression Using the Decay Rate, <i>ρ _pack, </i> and the Capsid Surfacic mass

<p>The estimates were identified by a stepwise regression among all parameters used. The order of entrance of parameters is an increasing function of <i>p</i>-values. The model explains 91% of the variance of the mortality rate. </p

Mortality Rates of Phage Particles

<div><p>(A) Representative survival curves of phage particles maintained in LB at 37 °C, in the absence of host cells. Phage stocks are obtained by infecting growing E. coli host culture followed by cell elimination. Lines show exponential regressions, with <i>R²</i> values ranging from 0.87 for P2 to 0.99 for MS2. The mortality rate is not influenced by the initial concentration of the phage populations (unpublished data). Each experiment was repeated at least three times independently. </p> <p>(B) Relation between mortality rate and temperature. Symbols are the same as in (A). Lines show exponential fits between the mortality rate and 1/T. <i>R²</i> values range from 0.937 for Mu to 0.999 for P2. </p></div

Representation of Various Phage Parameters in a PCA

<p>We can notice two groups of parameters: virion structural characteristics (green) and life history traits of phages (red). Within each group, parameters correlate highly with a nonparametric Spearman Rho test. For others correlations, see text and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040193#pbio-0040193-g004" target="_blank">Figure 4</a>. </p

Potential Relations between Phage Survival, Multiplication Rate, and Capsid Characteristics

<p>Evolutionary theory predicts that a high decay rate is associated with an elevated multiplication rate. Forces exerted on the capsid might lead to the rupture of the head of phages, leading to their inactivation. The multiplication rate of phages is possibly associated with properties of phage particles as a consequence of kinetic and energetic considerations involved in the assembly of the capsid and/or the encapsidation of the genome.</p

Transient advantage of virulent λ<i>cI</i>*phage.

<p>Evolution with time of the proportion of bacteria carrying the virulent λ<i>cI</i>* prophage (S^L) on bacteria carrying the λ<i>c</i>^ind- prophage (L). Means +/- standard error of the mean from 7 mice.</p

Estimated values of the model’s parameters.

<p>Estimated values of the model’s parameters.</p

Induction rate per lysogenic bacteria growing on rich medium (LB).

<p>The induction rate was measured on ampicillin plates by scoring infective centers, as described in the Materials and Methods section. Since bile salts were shown to cause DNA damage in bacteria [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005861#pgen.1005861.ref034" target="_blank">34</a>], and to induce a <i>Salmonella</i> prophage [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005861#pgen.1005861.ref035" target="_blank">35</a>], we measured their effect on λ induction rate, but no change was detected. Bile salts were added at a final concentration of 0.8%. Mean ± standard deviation of three independent experiments are indicated.</p

A high <i>in vivo</i> induction rate penalizes lysogens in the absence of susceptible bacteria.

<p>A) Evolution of the ratio of lysogen over susceptible lineages (L/(S+S^L)) in mice feces after day 2. Means +/- standard deviations from 8, 13 and 4 mice for initial L/S ratios (1:1, 1:10 and 1:100 respectively) are indicated. B) Evolution over 9 days of L/(S+S^L) ratio for wild-type λ prophage (brown line) or for λ<i>cI</i>^ind- deficient for induction (black line). Means +/- standard error of the mean from 7 and 12 mice for λ<i>cI</i>^ind- and wild-type respectively. C) Two-phase temporal simulation of L/(S+S^L) ratio, with a switch at 48h to a lamB^- version of the model (i.e. with a = 0). The ratio is shown for wild-type phage (red line) or λ<i>cI</i>^ind- mutant (blue line, with <i>x</i> = 2x10^-7). The initial condition for the first phase is taken from data at time 0, and the initial condition for the second phase (“mutant model”) is taken from experimental data at 48h.</p