Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli

Abstract

Twelve populations of Escherichia coli, derived from a common ancestor, evolved in a glucose-limited medium for 20,000 generations. Here we use DNA expression arrays to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation. We compared the expression profile of the ancestor to that of clones sampled from both populations after 20,000 generations. The expression of 59 genes had changed significantly in both populations. Remarkably, all 59 were changed in the same direction relative to the ancestor. Many of these genes were members of the cAMP-cAMP receptor protein (CRP) and guanosine tetraphosphate (ppGpp) regulons. Sequencing of several genes controlling the effectors of these regulons found a nonsynonymous mutation in spoT in one population. Moving this mutation into the ancestral background showed that it increased fitness and produced many of the expression changes manifest after 20,000 generations. The same mutation had no effect on fitness when introduced into the other evolved population, indicating that a mutation of similar effect was present already. Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations.

Figure 1

Pairwise comparisons of gene expression between evolved and ancestral clones. Both axes are log₁₀-transformed standardized expression levels. (a) Comparison of Ara⁻ and Ara⁺ ancestors. (b) Comparison of the Ara−1 clone from 20,000 generations and its ancestor. (c) Comparison of the Ara+1 clone from 20,000 generations and its ancestor. (d) Comparison of evolved Ara−1 and Ara+1 clones. (b and c) The colored points mark genes with expression that changed significantly (P < 0.05) relative to the ancestor in both evolved clones; genes with increased expression are shown in green, and genes with reduced expression are shown in red. The d values measure the overall divergence in expression profiles and were calculated as explained in Methods.

Figure 2

Predicted and observed divergence (d) in gene-expression profiles between two independently evolved clones. The predicted value was calculated as the sum of each clone's divergence from its ancestor. Error bars are 95% confidence intervals.

Figure 3

Nonsynonymous mutations in spoT in eight independently evolved E. coli populations. Only the variable amino acid residues are shown, with the ancestor listed first and the eight mutant alleles shown below. Four other populations retained the ancestral sequence. The maximum extent of the regions needed for ppGpp hydrolase and synthetase activities are shown along the top; the C terminus is hypothesized to regulate the relative activity of these two functions (36).