Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174

Abstract

Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages) has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones' phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution.

Keywords: evolutionary theory; genetics of adaptation; life history; lysis time; variance.

Figure 1

Typical serially sampled parallel infection assay data (pos5, ${\text{β}}_a$ = 0.71). Here, sampling was performed at 15-sec intervals between 5 min and 28.75 min. At each time point, three outcomes were possible: zero plaques, a “few” plaques (here, fewer than eight; see section Statistical methods), and more than a few. Assuming 100% plating efficiency, these outcomes implied respectively that no phage particles were added to the corresponding host cell volume; that the visible number of phage particles was added, but none lysed its host by the time of sampling; and that at least one infected cell had been lysed by the time of sampling. In these data, the first sample with more than a few plaques occurred at 15.5 min, giving an upper bound for the time to lysis ($t_0$). Inset illustrates plaque counts prior to the first observed lysis event. The absence of corresponding stratification among plaque counts after 15.5 min implied high variance in burst size. Similarly, the two plaques observed at 23.5 min (arrow) corresponded to two phage particles that had not yet lysed their hosts by that time, implying high variance in lysis time. Thus, these data contain information about higher moments in both burst size and lysis time.

Figure 2

Positions of mutations in φX174 genome. The figure shows a 832-bp region of interest, including genes C, D, E, and J. Gene C is involved in DNA replication, gene D is an external scaffolding protein required for procapsid morphogenesis, gene E is responsible for lysis of the host, and gene J is required for DNA packaging (Fane et al. 2006). Gene E is shown in three sections, corresponding to three domains of the protein. The transmembrane domain binds the E protein’s substrate, MraY (Mendel et al. 2006; Zheng et al. 2009). Mutations are indicated with pins at the position, and the site and nucleotide change are indicated to the right of the pin head. The clone(s) carrying each mutation is indicated in parentheses. Note that one of the five background nucleotide differences between the Epos and D-promoter mutants (G833A) is included in this figure.

Figure 3

Estimated cumulative lysis probability by time functions, pairwise comparisons of each clone with the wild type. The wild type panel (top left) provides an example of fitting a cumulative lysis probability by time function to wild-type data. The gray line is the best-fit curve. Dotted lines represent 100 of the 500 bootstrap replicates. Each bubble’s position shows the proportion of wells sampled at a given time in which we observe a lysis event; the size of each bubble shows the number of samples on which the proportion is based. In all other panels, the wild type is represented with a gray line and gray bubbles.

Figure 4

Estimates of parameters λ and $t_0$ that define the lysis probability function for wildtype and each mutant. Bars represent the approximate 95% confidence intervals for each parameter independent of the other (based on 500 bootstrap replicates).

Figure 5

Estimated burst size by time relationships for wild type and each mutant.