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

Abstract

A microbe’s ecological niche and biotechnological utility are confirmed 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. In this work, 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, indicating 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 reflect 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 thesemore » limitations.« less

Authors:
ORCiD logo [1];  [2];  [3];  [2];  [1];  [4]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [3]; ORCiD logo [2]; ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  3. Brandeis Univ., Waltham, MA (United States)
  4. Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Science Foundation (NSF)
OSTI Identifier:
1570140
Alternate Identifier(s):
OSTI ID: 1567911
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Molecular microbiology
Additional Journal Information:
Journal Name: Molecular microbiology; Journal ID: ISSN 0950-382X
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
biosystem design; pathway optimization; molecular dynamics; IMPDH; lignin catabolism

Citation Formats

Close, Dan, Cooper, Conner J., Wang, Xingyou, Chirania, Payal, Gupta, Madhulika, Ossyra, John R., Giannone, Richard J., Engle, Nancy L., Tschaplinski, Timothy J., Smith, Jeremy C., Hedstrom, Lizbeth, Parks, Jerry M., and Michener, Josh. Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. United States: N. p., 2019. Web. doi:10.1111/MMI.14393.
Close, Dan, Cooper, Conner J., Wang, Xingyou, Chirania, Payal, Gupta, Madhulika, Ossyra, John R., Giannone, Richard J., Engle, Nancy L., Tschaplinski, Timothy J., Smith, Jeremy C., Hedstrom, Lizbeth, Parks, Jerry M., & Michener, Josh. Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. United States. doi:10.1111/MMI.14393.
Close, Dan, Cooper, Conner J., Wang, Xingyou, Chirania, Payal, Gupta, Madhulika, Ossyra, John R., Giannone, Richard J., Engle, Nancy L., Tschaplinski, Timothy J., Smith, Jeremy C., Hedstrom, Lizbeth, Parks, Jerry M., and Michener, Josh. Wed . "Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis". United States. doi:10.1111/MMI.14393.
@article{osti_1570140,
title = {Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis},
author = {Close, Dan and Cooper, Conner J. and Wang, Xingyou and Chirania, Payal and Gupta, Madhulika and Ossyra, John R. and Giannone, Richard J. and Engle, Nancy L. and Tschaplinski, Timothy J. and Smith, Jeremy C. and Hedstrom, Lizbeth and Parks, Jerry M. and Michener, Josh},
abstractNote = {A microbe’s ecological niche and biotechnological utility are confirmed 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. In this work, 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, indicating 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 reflect 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.},
doi = {10.1111/MMI.14393},
journal = {Molecular microbiology},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {9}
}

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