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:

Close, Dan  ^[1];

• Search DOE PAGES for author "Close, Dan"
• Search DOE PAGES for ORCID "0000-0003-4790-4448"
• Search orcid.org for ORCID "0000-0003-4790-4448"

Cooper, Conner J. ^[2]; Wang, Xingyou ^[3]; Chirania, Payal ^[2]; Gupta, Madhulika ^[1]; Ossyra, John R. ^[4]; Giannone, Richard J.  ^[1];

• Search DOE PAGES for author "Giannone, Richard J."
• Search DOE PAGES for ORCID "0000-0001-8551-0138"
• Search orcid.org for ORCID "0000-0001-8551-0138"

Engle, Nancy L.  ^[1];

• Search DOE PAGES for author "Engle, Nancy L."
• Search DOE PAGES for ORCID "0000-0003-0290-7987"
• Search orcid.org for ORCID "0000-0003-0290-7987"

Tschaplinski, Timothy J.  ^[1];

• Search DOE PAGES for author "Tschaplinski, Timothy J."
• Search DOE PAGES for ORCID "0000-0002-9540-6622"
• Search orcid.org for ORCID "0000-0002-9540-6622"

Smith, Jeremy C.  ^[2];

• Search DOE PAGES for author "Smith, Jeremy C."
• Search DOE PAGES for ORCID "0000-0002-2978-3227"
• Search orcid.org for ORCID "0000-0002-2978-3227"

Hedstrom, Lizbeth ^[3]; Parks, Jerry M.  ^[2];

• Search DOE PAGES for author "Parks, Jerry M."
• Search DOE PAGES for ORCID "0000-0002-3103-9333"
• Search orcid.org for ORCID "0000-0002-3103-9333"

Michener, Josh  ^[1]

• Search DOE PAGES for author "Michener, Josh"
• Search DOE PAGES for ORCID "0000-0003-2302-8180"
• Search orcid.org for ORCID "0000-0003-2302-8180"

---

+ Show Author Affiliations

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:

2019-09-18

Research Org.:

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER); 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 Volume: 112; Journal Issue: 6; Journal ID: ISSN 0950-382X

Publisher:

Wiley

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; biosystem design; pathway optimization; molecular dynamics; IMPDH; lignin catabolism