Experimental Evolution of an Essential Bacillus Gene in an E. coli Host

Abstract

The acquisition of foreign genes by HGT potentially greatly speeds up adaptation by allowing faster evolution of beneficial traits. The evolutionary integration of novel genes into host gene expression and physiology is critical for adaptation by HGT, but remains largely unknown. We are exploring the evolutionary consequences of gene acquisition in populations of Escherichia coli in real time. A plasmid bearing the genes necessary for sucrose catabolism was constructed and introduced into a single E. coli genotype. Wild-type E. coli is generally incapable of utilizing sucrose, but E. coli transformants were able to grow on sucrose as a sole carbon and energy source, albeit poorly. Twelve replicate populations were initiated and propagated in sucrose minimal media for 300 generations. Over this time, we observed large fitness improvements in the selected environment. These results demonstrate the potential for HGT to substantially increase microbial niche breadth.

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

“…It has been suggested that as the number of nodes connecting an extant protein within its protein–protein interaction network increases, the capacity to replace that protein with another homolog decreases despite the presumed functional equivalence between the endogenous gene and the homolog (Jain et al 1999). Several orthologous protein substitution experiments demonstrated successful transfer of an alien gene to a foreign genome (Bershtein et al 2015; Larios-Sanz and Travisano 2009; Lind et al 2010), resulting in a fitness decrease similar to our approach, which was referred to as the “weak link approach” (Counago et al 2006). After evolving these organisms under laboratory conditions, it was demonstrated that direct accumulation of convergent mutations on the extant alien gene exhibits adaptive behavior (Counago et al 2006; Miller et al 2010; Pena et al 2010).…”

“…When challenged with an ancestral component, will the engineered bacteria accumulate direct mutations on the ancestral component and “re-trace” the evolutionary history of this component by changing its sequence to be closer to the modern variant (Lind et al 2010; Pena et al 2010)? Alternatively, are compensatory mutations non-directional due to the very large solution space, and therefore the organism may be expected to respond to the ancient perturbation through modifications and modulation outside of the ancestral gene-coding region (Larios-Sanz and Travisano 2009)? To what degree will the adaptive pathways of the modified organism recapitulate the organism’s evolutionary history and thus allow researchers to address the role of chance and necessity at the molecular level?…”

Experimental evolution of Escherichia coli harboring an ancient translation protein

“…When challenged with an ancestral component, will the engineered bacteria accumulate direct mutations on the ancestral component and "re-trace" the evolutionary history of this component by changing its sequence to be closer to the modern variant (Lind et al 2010;Pena et al 2010)? Alternatively, are compensatory mutations non-directional due to the very large solution space, and therefore the organism may be expected to respond to the ancient perturbation through modifications and modulation outside of the ancestral gene-coding region (Larios-Sanz and Travisano 2009) ? To what degree will the adaptive pathways of the modified organism recapitulate the organism's evolutionary history and thus allow Amino acid sequences were obtained from the NCBI database and aligned using Clustal Omega (Sievers et al 2011).…”