Parallel Changes in Global Protein Profiles During Long-Term Experimental Evolution in Escherichia coli

Abstract

Twelve populations of Escherichia coli evolved in and adapted to a glucose-limited environment from a common ancestor. We used two-dimensional protein electrophoresis to compare two evolved clones, isolated from independently derived populations after 20,000 generations. Exceptional parallelism was detected. We compared the observed changes in protein expression profiles with previously characterized global transcription profiles of the same clones; this is the first time such a comparison has been made in an evolutionary context where these changes are often quite subtle. The two methodologies exhibited some remarkable similarities that highlighted two different levels of parallel regulatory changes that were beneficial during the evolution experiment. First, at the higher level, both methods revealed extensive parallel changes in the same global regulatory network, reflecting the involvement of beneficial mutations in genes that control the ppGpp regulon. Second, both methods detected expression changes of identical gene sets that reflected parallel changes at a lower level of gene regulation. The protein profiles led to the discovery of beneficial mutations affecting the malT gene, with strong genetic parallelism across independently evolved populations. Functional and evolutionary analyses of these mutations revealed parallel phenotypic decreases in the maltose regulon expression and a high level of polymorphism at this locus in the evolved populations.

Experimental evolution of nodule intracellular infection in legume symbionts

“…The effect on infection of these three mutations was found to be contingent on the initial hrcV (T3SS À ) mutation carried by the CBM356 ancestor, reinforcing previous evidence that evolution is thrifty (Pelosi et al, 2006). The vsrA mutation alone did not allow the wild-type chimera CBM124 to nodulate, in agreement with the fact that vsrA does not control the T3SS.…”

Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol

“…2f). Interestingly, these are systemic and coordinated responses resulting from a single mutation showing that it acts through multiple mechanisms, as others have reported 2,23 .…”

Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator

“…The availability of technology to rapidly identify mutations in adapted strains, and then evaluate the contributions of those mutations to adaptation with genetic manipulation, has greatly accelerated the understanding of the mechanisms for adaptation to new substrates (Brockhurst et al, 2010). Genomic changes promoting adaptation to new substrates have included mutations that enhance the kinetics of enzymes acting on the substrate (Fong et al, 2005a, b;Herring et al, 2006;Conrad et al, 2009;Lee and Palsson, 2010) and mutations in promoter regions and global regulatory elements (Treves et al, 1998;Herring et al, 2006;Pelosi et al, 2006); as well as RNA polymerases (Herring et al, 2006;Conrad et al, 2010). Surprisingly, there have been fewer reports of adaptation to the use of a new substrate via mutations in known transcriptional regulators (Philippe et al, 2007;Barrick et al, 2009) despite the fact that changes in transcriptional regulators are thought to have key roles in the evolution of new microbial species (Dekel and Alon, 2005;Babu and Aravind, 2006;Babu et al, 2007), a concept further supported with the observation that transcriptional regulatory networks evolve and change faster than other collaborative biological networks such as protein interaction networks and metabolic pathway networks (Shou et al, 2011).…”