Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis

Abstract

Summary A microbe’s ecological niche and biotechnological utility are determined by its specific set of co‐evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. Here we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is resistant to inhibition by the relevant intermediate, suggesting that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single‐residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results demonstrate how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.

Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization ofPopulusroots

“…Given the high frequency of SA catabolism in these isolates, we sought to understand the factors limiting the dissemination or retention of this pathway in GM17. We initially hypothesized that deleterious interactions between a newly-introduced SA pathway and the native metabolic pathways of the potential hosts would prevent successful transfer into GM17 [30, 31]. To test this hypothesis, we engineered the SA catabolic pathway into several Pseudomonas isolates and measured changes in catabolic activity.…”