Journal Article

Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution

Duarte, José M, Isalan, Mark, Sharpe, James, Schaerli, Yolanda, Jiménez, Alba, Wagner, Andreas, Mihajlovic, Ljiljana, Renggli, Julien

2018

Overview

Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms behind such biases are still poorly understood. Gene regulatory networks have been proposed as one cause of constrained phenotypic variation. However, most pertinent evidence is theoretical rather than experimental. Here, we study evolutionary biases in two synthetic gene regulatory circuits expressed in Escherichia coli that produce a gene expression stripe—a pivotal pattern in embryonic development. The two parental circuits produce the same phenotype, but create it through different regulatory mechanisms. We show that mutations cause distinct novel phenotypes in the two networks and use a combination of experimental measurements, mathematical modelling and DNA sequencing to understand why mutations bring forth only some but not other novel gene expression phenotypes. Our results reveal that the regulatory mechanisms of networks restrict the possible phenotypic variation upon mutation. Consequently, seemingly equivalent networks can indeed be distinct in how they constrain the outcome of further evolution. Synopsis Analyses in synthetic circuits show that mutations result in distinct novel phenotypes in two circuits that showed the same phenotype before mutation. This constrained phenotypic variation is caused by differences in the circuits’ regulatory mechanisms. Two synthetic circuits expressed in E. coli that produce the same phenotype, but through different regulatory mechanisms, are used to study the molecular mechanisms underlying constrained phenotypic variation during evolution. The two networks create different spectra of novel phenotypes after mutation. A combination of experimental measurements, mathematical modeling and DNA sequencing shows that the regulatory mechanisms restrict the phenotypic variation that becomes accessible upon mutation. Graphical Abstract Analyses in synthetic circuits show that mutations result in distinct novel phenotypes in two circuits that showed the same phenotype before mutation. This constrained phenotypic variation is caused by differences in the circuits’ regulatory mechanisms.

• Publisher: Nature Publishing Group UK,EMBO Press,John Wiley and Sons Inc,Springer Nature
• Subject: Arabinose - metabolism / Arabinose - pharmacology / Biological Evolution / Circuits / Cloning, Molecular / constrained evolution / Culture Media - chemistry / Culture Media - pharmacology / Deoxyribonucleic acid / DNA / DNA sequencing / E coli / EMBO11 / EMBO15 / EMBO41 / Embryogenesis / Embryonic growth stage / epistasis / Escherichia coli - drug effects / Escherichia coli - genetics / Escherichia coli - metabolism / Evolution / Gene expression / Gene Expression Regulation / Gene Regulatory Networks / Genetic Variation / Genotype / Genotype & phenotype / Mathematical analysis / Mathematical models / Models, Genetic / Molecular modelling / Mutation / Networks / Phenotype / Phenotypes / Phenotypic variations / regulatory mechanisms / Regulatory mechanisms (biology) / Selection, Genetic / Synthetic Biology - methods / synthetic circuits