Adaptive Evolution ofEscherichia coliK-12 MG1655 during Growth on a Nonnative Carbon Source,l-1,2-Propanediol

Abstract

Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source, L-1,2-propanediol (L-1,2-PDO), for ϳ700 generations. We found that (i) experimental evolution of E. coli for ϳ700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to use L-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h ؊1 ; (ii) six mutations detected by whole-genome resequencing accumulated in the evolved E. coli mutant over the course of adaptive evolution on L-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS5 was inserted between two fuc regulons; (iv) two major mutations (mutations in fucO and its promoter) involved in L-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.

Adaptive laboratory evolution of ethanologenic Zymomonas mobilis strain tolerant to furfural and acetic acid inhibitors

“…Finally, two novel acetic acid and furfural tolerant strains (named ZMA7-2 and ZMF3-3, respectively) were obtained for further use. Currently, ALE strategy has been successfully used in S. cerevisiae (Cakar et al 2012;Demeke et al 2013;Dhar et al 2011;WallaceSalinas and Gorwa-Grauslund 2013) and E. coli (Hua et al 2007;Lee and Palsson 2010), which will lead to the activation of latent metabolic pathways, phenotype optimization, increasing environmental factor tolerance, and improving bacterial fitness (Dragosits and Mattanovich 2013;Portnoy et al 2011). However, the potential of ALE for other microorganisms is now being recognized.…”

“…However, little study was focused on development of a furfural-tolerant strain in Z. mobilis. Recently, adaptive laboratory evolution (ALE) emerged as a valuable method in metabolic engineering for strain development and optimization (Chatterjee and Yuan 2006;Conrad et al 2011;Dragosits and Mattanovich 2013;Pál et al 2005;Portnoy et al 2011), which has been successfully used in model organisms, such as Escherichia coli (Hua et al 2007;Lee and Palsson 2010) and Saccharomyces cerevisiae (Cakar et al 2012;Demeke et al 2013;Dhar et al 2011;Wallace-Salinas and Gorwa-Grauslund 2013). ALE is a powerful method to improve certain features of common industrial strains (e.g., inhibitor tolerance, substrate utilization, growth temperature) without requiring knowledge of any underlying genetic mechanisms, as long as the desired trait can be coupled with growth.…”

Functional and Metabolic Effects of Adaptive Glycerol Kinase (GLPK) Mutants in Escherichia coli

“…As described elsewhere (20,21), RNA was isolated using Qiagen RNAprotect and RNeasy kit and 10 g of RNA was converted to cDNA using random hexamers and Invitrogen SuperScript II reverse transcriptase. Each quantitative PCR (qPCR) reaction contained 5-10 ng of cDNA, 0.3 M of each primer, and 12.5 l of 2ϫ SYBR Master Mix (Qiagen) (see supplemental Table S1 for primer sequences).…”

Selection for Growth on 3-Nitrotoluene by 2-Nitrotoluene-Utilizing Acidovorax sp. Strain JS42 Identifies Nitroarene Dioxygenases with Altered Specificities

“…Bacteria are known for the ability to adapt to the presence of nonnative carbon and energy sources (54,55). Moreover, bacteria exposed to toxic synthetic chemicals in the environment evolve to take advantage of these potential sources of carbon and energy by developing new catabolic pathways (19,(56)(57)(58)(59).…”