The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape

<div><p>The fitness effect of mutations can be influenced by their interactions with the environment, other mutations, or both. Previously, we constructed 32 ( = 2⁵) genotypes that comprise all possible combinations of the first five beneficial mutations to fix in a laboratory-evolved population of <i>Escherichia coli</i>. We found that (i) all five mutations were beneficial for the background on which they occurred; (ii) interactions between mutations drove a diminishing returns type epistasis, whereby epistasis became increasingly antagonistic as the expected fitness of a genotype increased; and (iii) the adaptive landscape revealed by the mutation combinations was smooth, having a single global fitness peak. Here we examine how the environment influences epistasis by determining the interactions between the same mutations in two alternative environments, selected from among 1,920 screened environments, that produced the largest increase or decrease in fitness of the most derived genotype. Some general features of the interactions were consistent: mutations tended to remain beneficial and the overall pattern of epistasis was of diminishing returns. Other features depended on the environment; in particular, several mutations were deleterious when added to specific genotypes, indicating the presence of antagonistic interactions that were absent in the original selection environment. Antagonism was not caused by consistent pleiotropic effects of individual mutations but rather by changing interactions between mutations. Our results demonstrate that understanding adaptation in changing environments will require consideration of the combined effect of epistasis and pleiotropy across environments.</p></div

The five mutations in the order in that they arose and fixed in a population of <i>E. coli</i> from Lenski et al. 2002.

*<p> Relative fitness in DM25, experimental evolution conditions, relative to the ancestor, REL606.</p>1<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426-Cooper2" target="_blank">[39]</a>, </p>2<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426-Crozat1" target="_blank">[62]</a>, </p>3<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426-Pelosi1" target="_blank">[65]</a>, </p>4<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426-Lenski4" target="_blank">[66]</a>, </p>5<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426-Stanek1" target="_blank">[61]</a>, </p>6<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426-Schneider1" target="_blank">[57]</a>.</p

Distributions of epistatic effects in two environments.

<p>Observed and expected fitness were compared for 26 genotypes containing two or more mutations in two environments. Absolute epistasis was calculated as described in the text.</p

Effects of beneficial mutations in alternative environments.

<p>Genotypes are designated as single letters and define alleles: <i>rbs</i> (r), <i>topA</i> (t), <i>spot</i> (s), <i>glmS</i> (g), and <i>pykF</i> (p). Fill color defines the environment: black, DM25, white, EGTA, and grey, guanazole. Mutational effects were determined to depend on the environment using an ANOVA. Asterisks represent significance based on a <i>P</i> value < 0.05.</p

Distribution of gene relatedness and network size in the <i>E. coli</i> CLR network.

<p>(A) Probability distribution of relatedness values, , between pairs of genes in <i>E. coli</i> calculated using the CLR algorithm and the full dataset. (B) Size of the largest connected component for relatedness value, . At small values of the network is fully connected but begins to break up into multiple disconnected components at a critical value of approximately .</p

Links connecting operons in the community that enriches for genes involved in ribosome structure.

<p>CLR links are in light blue, RegulonDB links are in black. Small symbols are genes that are not in the community, but are regulators of genes that are in the community and are therefore candidates for mediating indirect interactions between community genes. Symbol shape and color indicate attributes as follows: red, transcription factors; dark blue, ppGpp regulated promoter by direct assay <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002391#pcbi.1002391-Lemke1" target="_blank">[54]</a>; light blue, ppGpp regulated translation related promoter by microarray <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002391#pcbi.1002391-Traxler1" target="_blank">[55]</a>; pink, other; hexagon, promoter; diamond, promoter; square, promoter; circle, unknown sigma factor. Note that very few interactions observed in the CLR network can be explained by the direct interactions annotated in RegulonDB. The high proportion of ppGpp sensitive promoters among operons contained in the community suggests this molecule as a good candidate for regulating the remaining interactions. The network layout was determined by the circular layout option in Cytoscape 2.8.1, no particular significance should be attached to operons being outside the main circle.</p

Populations_Fitness_Data

Results of competition experiments designed to estimate the fitness of evolving E. coli populations relative to their common ancesto

The magnitude and direction of epistatic effects on growth vary with external environment.

<p>Symbols represent growth (AUC) of a particular genotype relative to the ancestor (triangles = gp, circles = rtsgp). Filled symbols represent expected relative growth and open symbols represent observed relative growth based on a multiplicative model assuming no epistatic interactions. Differences between observed and expected values were determined using the t statistic (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426.s013" target="_blank">Table S9</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003426#pgen.1003426.s014" target="_blank">S10</a>).</p

Relationship between relative epistasis and expected fitness assuming no epistasis in each foreign environment.

<p>Each point refers to one of the 32 genotypes assayed for fitness in both environments (a, EGTA, b, guanazole). Error bars represent the standard deviation approximated through the method of error propagation. The solid lines are the best linear fit with the text below reporting the correlation (<i>r</i>) and significance (<i>P</i> values).</p

The 25 most relevant relationships found for without noise.

<p>The “P value” or random probability, calculated with a hypergeometric test with Benjamini-Hochberg correction, of the common occurrence, or overlap, of genes in an inferred community and in a GO term for the 25 most statistically relevant relationships are listed. Also listed are the “GO term num” that distinguishes the GO term and its “Description” in the GO database, the number of genes in the GO term “GO size”, the number of genes in the inferred community “Com size”, and the number of genes they have in common “In common.” The complete set of the 239 relevant relationships found for , as well as the relevant relationships found for , are given in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002391#pcbi.1002391.s007" target="_blank">Dataset S7</a>.</p