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

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.

The genetic basis of parallel and divergent phenotypic responses in evolving populations ofEscherichia coli

“…(ii) One spoT mutation found in our study is identical to a mutation previously found in one of the long-term populations (Cooper et al 2003); that previous clone has several other mutations that are not present in our clone, and thus we are certain that the exact same spoT mutation arose independently in these two populations. Given that these few identical mutations evolved independently, we retained them in most of our statistical analyses.…”

“…More generally, the relative scarcity of beneficial mutations in the synthetase and hydrolase regions, as opposed to the C-terminal regulatory domain (figure 2a), may reflect functional constraints on the types of mutations that can produce the beneficial effect. This concentration of beneficial mutations in the C-terminal domain is seen not only among the mutations found in these single mutation clones (11 out of 13 spoT mutations in this domain) but also in the lines that evolved for 20 000 generations during a long-term experiment in the same environment (6 out of 8 mutations in this domain; Cooper et al 2003).…”

“…For the single mutation lines analysed here and from a previous analysis of this gene in the long-term lines Cooper et al 2003) and associated with the first selective sweep within 400 generations (bottom; this study). Clone identification numbers listed in table S1 in the electronic supplementary material are abbreviated here to include only their last two digits, which are unique to each clone (e.g.…”

“…(c) DNA sequencing Previous analyses of a long-term evolution experiment, initiated from the same ancestor and employing the same glucose-limited environment, identified five genes or gene regions as candidate loci for adaptation: pykF; nadR; hokB/sokB; spoT; and an upstream non-coding region of pbpA-rodA (Schneider et al 2000;Cooper et al 2001Cooper et al , 2003Woods et al 2006). Primers were designed to cover the overlapping regions of these genes or gene regions.…”

Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle

“…For example, shifting replicate microbial populations to novel environments can produce repeatable modification of traits, through either similar or distinct genetic changes (Cooper et al 2003;Travisano et al 1995;Wichman et al 1999). Less is known about the degree of parallelism underlying the convergence of complex, polygenic characters, such as behaviors (Bult and Lynch 1996).…”