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

Dan M. Close, Connor J. Cooper, Xingyou Wang, Payal Chirania, Madhulika Gupta, John R. Ossyra, Richard J. Giannone, Nancy Engle, Timothy J. Tschaplinski, Jeremy C. Smith, Lizbeth Hedstrom, Jerry M. Parks, Joshua K. Michener

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

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.

Original languageEnglish
Pages (from-to)1784-1797
Number of pages14
JournalMolecular Microbiology
Volume112
Issue number6
DOIs
StatePublished - Dec 1 2019

Funding

Genome resequencing and analysis was performed by Christa Pennacchio, Natasha Brown, Anna Lipzen and Wendy Schackwitz at the Joint Genome Institute. DNA synthesis was performed by Jan-Fang Cheng, Samuel Deutsch and Miranda Harmon-Smith at the Joint Genome Institute. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. CJC was supported by NIH/NIGMS-IMSD Grant No. R25GM086761. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. (2017219379). This work was supported by the BioEnergy Science Center and The Center for Bioenergy Innovation, both U.S. Department of Energy Research Centers supported by the Office of Biological and Environmental Research in the DOE Office of Science; the National Institutes of Health (GM054403 to LH); and the ORNL Laboratory Directed Research and Development program. This work also used resources of the Compute and Data Environment for Science (CADES) and the Oak Ridge Leadership Computing Facility (OLCF) at ORNL. Oak Ridge National Laboratory (ORNL) is managed by UT-Battelle, LLC, for the DOE under Contract No. DE-AC05-00OR22725.

Fingerprint

Dive into the research topics of 'Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis'. Together they form a unique fingerprint.

Cite this