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Mol Microbiol. 2019 Sep 18. doi: 10.1111/mmi.14393. [Epub ahead of print]

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

Author information

1
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
2
Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
3
Graduate Program in Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA.
4
Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
5
BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
6
Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
7
Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee, 37996, USA.
8
Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02454, USA.
9
Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA.

Abstract

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.

PMID:
31532038
DOI:
10.1111/mmi.14393

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