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Title: Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families

Abstract

Metagenomics has made accessible an enormous reserve of global biochemical diversity. In order to tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. Here, we validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.

Authors:
 [1];  [2];  [1];  [1];  [3];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [4];  [5];  [6];  [3];  [7];  [2];  [1];  [2] more »;  [1] « less
  1. Univ. of Toronto, ON (Canada). Dept. of Chemical Engineering and Applied Chemistry
  2. Bangor Univ., Gwynedd (United Kingdom). School of Biological Sciences
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structural Genomics, Structural Biology Center
  4. Univ. of Evry Val d'Essonne (UEVE) (France). National Center of Scientific Research (CNRS)
  5. Univ. of Evry Val d'Essonne (UEVE) (France). National Center for Scientific Research (CNRS)
  6. Inst. for Coastal Marine Environment, Messina (Italy)
  7. Spanish National Research Council (CSIC), Madrid (Spain). Inst. of Catalysis
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); Genome Canada; Ontario Genomics Institute; Ontario Research Fund; Natural Sciences and Engineering Research Council of Canada (NSERC); Spanish Ministerio de Economia y Competitividad (MINECO); German Federal Ministry of Education and Research (BMBF); Biotechnology and Biological Sciences Research Council (BBSRC); European Regional Development Fund (ERDF)
OSTI Identifier:
1393927
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; expression systems; hydrolases; x-ray crystallography

Citation Formats

Popovic, Ana, Hai, Tran, Tchigvintsev, Anatoly, Hajighasemi, Mahbod, Nocek, Boguslaw, Khusnutdinova, Anna N., Brown, Greg, Glinos, Julia, Flick, Robert, Skarina, Tatiana, Chernikova, Tatyana N., Yim, Veronica, Brüls, Thomas, Paslier, Denis Le, Yakimov, Michail M., Joachimiak, Andrzej, Ferrer, Manuel, Golyshina, Olga V., Savchenko, Alexei, Golyshin, Peter N., and Yakunin, Alexander F.. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. United States: N. p., 2017. Web. https://doi.org/10.1038/srep44103.
Popovic, Ana, Hai, Tran, Tchigvintsev, Anatoly, Hajighasemi, Mahbod, Nocek, Boguslaw, Khusnutdinova, Anna N., Brown, Greg, Glinos, Julia, Flick, Robert, Skarina, Tatiana, Chernikova, Tatyana N., Yim, Veronica, Brüls, Thomas, Paslier, Denis Le, Yakimov, Michail M., Joachimiak, Andrzej, Ferrer, Manuel, Golyshina, Olga V., Savchenko, Alexei, Golyshin, Peter N., & Yakunin, Alexander F.. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. United States. https://doi.org/10.1038/srep44103
Popovic, Ana, Hai, Tran, Tchigvintsev, Anatoly, Hajighasemi, Mahbod, Nocek, Boguslaw, Khusnutdinova, Anna N., Brown, Greg, Glinos, Julia, Flick, Robert, Skarina, Tatiana, Chernikova, Tatyana N., Yim, Veronica, Brüls, Thomas, Paslier, Denis Le, Yakimov, Michail M., Joachimiak, Andrzej, Ferrer, Manuel, Golyshina, Olga V., Savchenko, Alexei, Golyshin, Peter N., and Yakunin, Alexander F.. Wed . "Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families". United States. https://doi.org/10.1038/srep44103. https://www.osti.gov/servlets/purl/1393927.
@article{osti_1393927,
title = {Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families},
author = {Popovic, Ana and Hai, Tran and Tchigvintsev, Anatoly and Hajighasemi, Mahbod and Nocek, Boguslaw and Khusnutdinova, Anna N. and Brown, Greg and Glinos, Julia and Flick, Robert and Skarina, Tatiana and Chernikova, Tatyana N. and Yim, Veronica and Brüls, Thomas and Paslier, Denis Le and Yakimov, Michail M. and Joachimiak, Andrzej and Ferrer, Manuel and Golyshina, Olga V. and Savchenko, Alexei and Golyshin, Peter N. and Yakunin, Alexander F.},
abstractNote = {Metagenomics has made accessible an enormous reserve of global biochemical diversity. In order to tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. Here, we validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.},
doi = {10.1038/srep44103},
journal = {Scientific Reports},
number = ,
volume = 7,
place = {United States},
year = {2017},
month = {3}
}

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