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Title: A metabolic pathway for catabolizing levulinic acid in bacteria

Abstract

Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. Here, this discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [2];  [2];  [2];  [3];  [2];  [1]; ORCiD logo [1]
  1. Univ. of Wisconsin, Madison, WI (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1399002
Grant/Contract Number:
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Microbiology
Additional Journal Information:
Journal Volume: 2; Journal ID: ISSN 2058-5276
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Rand, Jacqueline M., Pisithkul, Tippapha, Clark, Ryan L., Thiede, Joshua M., Mehrer, Christopher R., Agnew, Daniel E., Campbell, Candace E., Markley, Andrew L., Price, Morgan N., Ray, Jayashree, Wetmore, Kelly M., Suh, Yumi, Arkin, Adam P., Deutschbauer, Adam M., Amador-Noguez, Daniel, and Pfleger, Brian F. A metabolic pathway for catabolizing levulinic acid in bacteria. United States: N. p., 2017. Web. doi:10.1038/s41564-017-0028-z.
Rand, Jacqueline M., Pisithkul, Tippapha, Clark, Ryan L., Thiede, Joshua M., Mehrer, Christopher R., Agnew, Daniel E., Campbell, Candace E., Markley, Andrew L., Price, Morgan N., Ray, Jayashree, Wetmore, Kelly M., Suh, Yumi, Arkin, Adam P., Deutschbauer, Adam M., Amador-Noguez, Daniel, & Pfleger, Brian F. A metabolic pathway for catabolizing levulinic acid in bacteria. United States. doi:10.1038/s41564-017-0028-z.
Rand, Jacqueline M., Pisithkul, Tippapha, Clark, Ryan L., Thiede, Joshua M., Mehrer, Christopher R., Agnew, Daniel E., Campbell, Candace E., Markley, Andrew L., Price, Morgan N., Ray, Jayashree, Wetmore, Kelly M., Suh, Yumi, Arkin, Adam P., Deutschbauer, Adam M., Amador-Noguez, Daniel, and Pfleger, Brian F. 2017. "A metabolic pathway for catabolizing levulinic acid in bacteria". United States. doi:10.1038/s41564-017-0028-z.
@article{osti_1399002,
title = {A metabolic pathway for catabolizing levulinic acid in bacteria},
author = {Rand, Jacqueline M. and Pisithkul, Tippapha and Clark, Ryan L. and Thiede, Joshua M. and Mehrer, Christopher R. and Agnew, Daniel E. and Campbell, Candace E. and Markley, Andrew L. and Price, Morgan N. and Ray, Jayashree and Wetmore, Kelly M. and Suh, Yumi and Arkin, Adam P. and Deutschbauer, Adam M. and Amador-Noguez, Daniel and Pfleger, Brian F.},
abstractNote = {Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. Here, this discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.},
doi = {10.1038/s41564-017-0028-z},
journal = {Nature Microbiology},
number = ,
volume = 2,
place = {United States},
year = 2017,
month = 9
}

Journal Article:
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