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Title: Discovery of enzymes for toluene synthesis from anoxic microbial communities

Abstract

Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic-hydrocarbon-producing enzymes, and will enable first-time biochemical synthesis of an aromatic fuel hydrocarbon from renewable resources, such as lignocellulosic biomass, rather than from petroleum.

Authors:
ORCiD logo [1];  [2];  [2]; ORCiD logo [3];  [2];  [2];  [1];  [4]; ORCiD logo [5]; ORCiD logo [2]; ORCiD logo [6]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  3. Taipei Medical Univ. (Taiwan)
  4. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Technical Univ. of Denmark, Lyngby (Denmark)
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:
1530356
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Chemical Biology
Additional Journal Information:
Journal Volume: 14; Journal Issue: 5; Journal ID: ISSN 1552-4450
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Beller, Harry R., Rodrigues, Andria V., Zargar, Kamrun, Wu, Yu-Wei, Saini, Avneesh K., Saville, Renee M., Pereira, Jose H., Adams, Paul D., Tringe, Susannah G., Petzold, Christopher J., and Keasling, Jay D. Discovery of enzymes for toluene synthesis from anoxic microbial communities. United States: N. p., 2018. Web. doi:10.1038/s41589-018-0017-4.
Beller, Harry R., Rodrigues, Andria V., Zargar, Kamrun, Wu, Yu-Wei, Saini, Avneesh K., Saville, Renee M., Pereira, Jose H., Adams, Paul D., Tringe, Susannah G., Petzold, Christopher J., & Keasling, Jay D. Discovery of enzymes for toluene synthesis from anoxic microbial communities. United States. doi:10.1038/s41589-018-0017-4.
Beller, Harry R., Rodrigues, Andria V., Zargar, Kamrun, Wu, Yu-Wei, Saini, Avneesh K., Saville, Renee M., Pereira, Jose H., Adams, Paul D., Tringe, Susannah G., Petzold, Christopher J., and Keasling, Jay D. Mon . "Discovery of enzymes for toluene synthesis from anoxic microbial communities". United States. doi:10.1038/s41589-018-0017-4. https://www.osti.gov/servlets/purl/1530356.
@article{osti_1530356,
title = {Discovery of enzymes for toluene synthesis from anoxic microbial communities},
author = {Beller, Harry R. and Rodrigues, Andria V. and Zargar, Kamrun and Wu, Yu-Wei and Saini, Avneesh K. and Saville, Renee M. and Pereira, Jose H. and Adams, Paul D. and Tringe, Susannah G. and Petzold, Christopher J. and Keasling, Jay D.},
abstractNote = {Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic-hydrocarbon-producing enzymes, and will enable first-time biochemical synthesis of an aromatic fuel hydrocarbon from renewable resources, such as lignocellulosic biomass, rather than from petroleum.},
doi = {10.1038/s41589-018-0017-4},
journal = {Nature Chemical Biology},
number = 5,
volume = 14,
place = {United States},
year = {2018},
month = {3}
}

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Cited by: 14 works
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