Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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
+ Show Author Affiliations
  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 Laboratory (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. doi:10.1038/srep44103.
Copy to clipboard
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
Copy to clipboard
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.
Copy to clipboard
@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 = {Wed Mar 08 00:00:00 EST 2017},
month = {Wed Mar 08 00:00:00 EST 2017}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/srep44103
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 48 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms
journal, June 2000

Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis
journal, September 2007

  • Nocek, B.; Mulligan, R.; Bargassa, M.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 70, Issue 1
  • DOI: 10.1002/prot.21276

Miscellaneous Algorithms for Density Modification
journal, July 1998

  • Cowtan, Kevin; Main, Peter
  • Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 4
  • DOI: 10.1107/s0907444997011980

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Fast Fourier feature recognition
journal, September 2001

  • Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 10
  • DOI: 10.1107/s0907444901010812

Bacterial Biocatalysts: Molecular Biology, Three-Dimensional Structures, and Biotechnological Applications of Lipases
journal, October 1999

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
journal, March 2007

Protein-protein interactions: methods for detection and analysis.
journal, January 1995

Nature of the protein universe
journal, June 2009

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results
journal, December 2005

  • Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf
  • Journal of Synchrotron Radiation, Vol. 13, Issue 1
  • DOI: 10.1107/S0909049505036721

Identification and characterization of novel poly(dl-lactic acid) depolymerases from metagenome
journal, July 2008

  • Mayumi, Daisuke; Akutsu-Shigeno, Yukie; Uchiyama, Hiroo
  • Applied Microbiology and Biotechnology, Vol. 79, Issue 5
  • DOI: 10.1007/s00253-008-1477-3

ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions
journal, November 2012

  • Lenfant, Nicolas; Hotelier, Thierry; Velluet, Eric
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1154

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008

A human gut microbial gene catalogue established by metagenomic sequencing
journal, March 2010

  • Qin, Junjie; Li, Ruiqiang; Raes, Jeroen
  • Nature, Vol. 464, Issue 7285
  • DOI: 10.1038/nature08821

Metagenomics: Application of Genomics to Uncultured Microorganisms
journal, March 2005

Psychrophilic enzymes: hot topics in cold adaptation
journal, December 2003

  • Feller, Georges; Gerday, Charles
  • Nature Reviews Microbiology, Vol. 1, Issue 3
  • DOI: 10.1038/nrmicro773

Who's your neighbor? New computational approaches for functional genomics
journal, June 2000

  • Galperin, Michael Y.; Koonin, Eugene V.
  • Nature Biotechnology, Vol. 18, Issue 6
  • DOI: 10.1038/76443

Biochemical Characterization and Structural Analysis of a Highly Proficient Cocaine Esterase † , ‡
journal, October 2002

  • Turner, James M.; Larsen, Nicholas A.; Basran, Amrik
  • Biochemistry, Vol. 41, Issue 41
  • DOI: 10.1021/bi026131p

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome
journal, January 2015

  • Privé, Florence; Newbold, C. Jamie; Kaderbhai, Naheed N.
  • Applied Microbiology and Biotechnology, Vol. 99, Issue 13
  • DOI: 10.1007/s00253-014-6355-6

Mining enzymes from extreme environments
journal, June 2007

  • Ferrer, Manuel; Golyshina, Olga; Beloqui, Ana
  • Current Opinion in Microbiology, Vol. 10, Issue 3
  • DOI: 10.1016/j.mib.2007.05.004

Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.
journal, April 1996

  • Herzberg, O.; Chen, C. C.; Kapadia, G.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 7
  • DOI: 10.1073/pnas.93.7.2652

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Functional metagenomics for enzyme discovery: challenges to efficient screening
journal, December 2009

Enzyme genomics: Application of general enzymatic screens to discover new enzymes
journal, April 2005

  • Kuznetsova, Ekaterina; Proudfoot, Michael; Sanders, Stephen A.
  • FEMS Microbiology Reviews, Vol. 29, Issue 2
  • DOI: 10.1016/j.fmrre.2004.12.006

Enzyme genomics: Application of general enzymatic screens to discover new enzymes
journal, April 2005

Cloning and Identification of a New Group Esterase (Est5S) from Noncultured Rumen Bacterium
journal, August 2012

Est10: A Novel Alkaline Esterase Isolated from Bovine Rumen Belonging to the New Family XV of Lipolytic Enzymes
journal, May 2015

Cold-Adapted Enzymes
book, January 2006

Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis
journal, September 2020

The CCP4 suite programs for protein crystallography
journal, September 1994

Cold-Adapted Enzymes
journal, June 2006

Metagenomics approaches in systems microbiology
journal, January 2009

Increased Flexibility as a Strategy for Cold Adaptation: A COMPARATIVE MOLECULAR DYNAMICS STUDY OF COLD- AND WARM-ACTIVE URACIL DNA GLYCOSYLASE
journal, March 2005

  • Olufsen, Magne; Smalås, Arne O.; Moe, Elin
  • Journal of Biological Chemistry, Vol. 280, Issue 18
  • DOI: 10.1074/jbc.M500948200

A novel family VIII carboxylesterase derived from a leachate metagenome library exhibits promiscuous β-lactamase activity on nitrocefin
journal, June 2009

  • Rashamuse, Konanani; Magomani, Victoria; Ronneburg, Tina
  • Applied Microbiology and Biotechnology, Vol. 83, Issue 3
  • DOI: 10.1007/s00253-009-1895-x

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016

  • Letunic, Ivica; Bork, Peer
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw290

Bacterial lipolytic enzymes: classification and properties
journal, October 1999

trans-Dienelactone hydrolase from Pseudomonas reinekei MT1, a novel zinc-dependent hydrolase
journal, November 2008

  • Cámara, Beatriz; Marín, Macarena; Schlömann, Michael
  • Biochemical and Biophysical Research Communications, Vol. 376, Issue 2
  • DOI: 10.1016/j.bbrc.2008.09.006

Bacterial lipolytic enzymes: classification and properties
journal, September 1999

  • Arpigny, Jean Louis; Jaeger, Karl-Erich
  • Biochemical Journal, Vol. 343, Issue 1
  • DOI: 10.1042/bj3430177

Metagenomics and industrial applications
journal, June 2005

  • Lorenz, Patrick; Eck, Jürgen
  • Nature Reviews Microbiology, Vol. 3, Issue 6
  • DOI: 10.1038/nrmicro1161

HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes
journal, July 2006

  • Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
  • DOI: 10.1107/S0907444906019949

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Specific and sensitive plate assay for bacterial lipases.
journal, January 1987

Est10: A Novel Alkaline Esterase Isolated from Bovine Rumen Belonging to the New Family XV of Lipolytic Enzymes
journal, May 2015

trans-Dienelactone hydrolase from Pseudomonas reinekei MT1, a novel zinc-dependent hydrolase
journal, November 2008

  • Cámara, Beatriz; Marín, Macarena; Schlömann, Michael
  • Biochemical and Biophysical Research Communications, Vol. 376, Issue 2
  • DOI: 10.1016/j.bbrc.2008.09.006

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Cloning and Sequencing of a Poly(dl-Lactic Acid) Depolymerase Gene from Paenibacillus amylolyticus Strain TB-13 and Its Functional Expression in Escherichia coli
journal, May 2003

  • Akutsu-Shigeno, Yukie; Teeraphatpornchai, Teerawat; Teamtisong, Kamonluck
  • Applied and Environmental Microbiology, Vol. 69, Issue 5
  • DOI: 10.1128/AEM.69.5.2498-2504.2003

Indication for a New Lipolytic Enzyme Family: Isolation and Characterization of Two Esterases from a Metagenomic Library
journal, January 2010

  • Bayer, Sally; Kunert, Anja; Ballschmiter, Meike
  • Journal of Molecular Microbiology and Biotechnology, Vol. 18, Issue 3
  • DOI: 10.1159/000315459

Biochemical Characterization and Structural Analysis of a Highly Proficient Cocaine Esterase † , ‡
journal, October 2002

  • Turner, James M.; Larsen, Nicholas A.; Basran, Amrik
  • Biochemistry, Vol. 41, Issue 41
  • DOI: 10.1021/bi026131p

A Proton Wire and Water Channel Revealed in the Crystal Structure of Isatin Hydrolase
journal, June 2014

  • Bjerregaard-Andersen, Kaare; Sommer, Theis; Jensen, Jan K.
  • Journal of Biological Chemistry, Vol. 289, Issue 31
  • DOI: 10.1074/jbc.m114.568824

Enzyme genomics: Application of general enzymatic screens to discover new enzymes
journal, April 2005

Microbial carboxyl esterases: classification, properties and application in biocatalysis
journal, March 2002

Experimental phasing with SHELXC / D / E : combining chain tracing with density modification
journal, March 2010

  • Sheldrick, George M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444909038360

HMMER web server: interactive sequence similarity searching
journal, May 2011

  • Finn, R. D.; Clements, J.; Eddy, S. R.
  • Nucleic Acids Research, Vol. 39, Issue suppl
  • DOI: 10.1093/nar/gkr367

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Pfam: the protein families database
journal, November 2013

  • Finn, Robert D.; Bateman, Alex; Clements, Jody
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1223

Molecular Basis of Formaldehyde Detoxification: CHARACTERIZATION OF TWO S-FORMYLGLUTATHIONE HYDROLASES FROM ESCHERICHIA COLI, FrmB AND YeiG
journal, March 2006

  • Gonzalez, Claudio F.; Proudfoot, Michael; Brown, Greg
  • Journal of Biological Chemistry, Vol. 281, Issue 20
  • DOI: 10.1074/jbc.M600996200

A new esterase EstD2 isolated from plant rhizosphere soil metagenome
journal, August 2010

  • Lee, Myung Hwan; Hong, Kyung Sik; Malhotra, Shweta
  • Applied Microbiology and Biotechnology, Vol. 88, Issue 5
  • DOI: 10.1007/s00253-010-2729-6

Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats: Enzyme adaptation to poly-extremes
journal, December 2014

  • Alcaide, María; Stogios, Peter J.; Lafraya, Álvaro
  • Environmental Microbiology, Vol. 17, Issue 2
  • DOI: 10.1111/1462-2920.12660

The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes
journal, September 2014

  • Tchigvintsev, Anatoli; Tran, Hai; Popovic, Ana
  • Applied Microbiology and Biotechnology, Vol. 99, Issue 5
  • DOI: 10.1007/s00253-014-6038-3

The Uncultured Microbial Majority
journal, October 2003

Novel Polyphenol Oxidase Mined from a Metagenome Expression Library of Bovine Rumen: BIOCHEMICAL PROPERTIES, STRUCTURAL ANALYSIS, AND PHYLOGENETIC RELATIONSHIPS
journal, June 2006

  • Beloqui, Ana; Pita, Marcos; Polaina, Julio
  • Journal of Biological Chemistry, Vol. 281, Issue 32
  • DOI: 10.1074/jbc.M600577200

Functional and structural studies of a novel cold-adapted esterase from an Arctic intertidal metagenomic library
journal, July 2012

  • Fu, Juan; Leiros, Hanna-Kirsti S.; de Pascale, Donatella
  • Applied Microbiology and Biotechnology, Vol. 97, Issue 9
  • DOI: 10.1007/s00253-012-4276-9

Bacterial Biocatalysts: Molecular Biology, Three-Dimensional Structures, and Biotechnological Applications of Lipases
journal, October 1999

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

"Candidatus Cloacamonas Acidaminovorans": Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division
journal, February 2008

  • Pelletier, E.; Kreimeyer, A.; Bocs, S.
  • Journal of Bacteriology, Vol. 190, Issue 7
  • DOI: 10.1128/JB.01248-07

Identifying bacterial genes and endosymbiont DNA with Glimmer
journal, January 2007

Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormone-sensitive lipase
journal, April 1999

  • Derewenda, Zygmunt S.; Wei, Yunyi; Contreras, Juan Antonio
  • Nature Structural Biology, Vol. 6, Issue 4, p. 340-345
  • DOI: 10.1038/7576

The oligomeric structures of plant cryptochromes
journal, May 2020

Metagenomics approaches in systems microbiology
journal, January 2009

Exploring Nitrilase Sequence Space for Enantioselective Catalysis
journal, April 2004

Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the α/β hydrolase family
journal, July 2013

  • Alcaide, María; Tornés, Jesús; Stogios, Peter J.
  • Biochemical Journal, Vol. 454, Issue 1
  • DOI: 10.1042/BJ20130552

Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis
journal, September 2007

  • Nocek, B.; Mulligan, R.; Bargassa, M.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 70, Issue 1
  • DOI: 10.1002/prot.21276

Metagenomics: Application of Genomics to Uncultured Microorganisms
journal, December 2004

α/β Hydrolase fold enzymes: the family keeps growing
journal, December 1999

Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
journal, January 1995

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome
journal, January 2015

  • Privé, Florence; Newbold, C. Jamie; Kaderbhai, Naheed N.
  • Applied Microbiology and Biotechnology, Vol. 99, Issue 13
  • DOI: 10.1007/s00253-014-6355-6

Psychrophilic enzymes: hot topics in cold adaptation
journal, December 2003

  • Feller, Georges; Gerday, Charles
  • Nature Reviews Microbiology, Vol. 1, Issue 3
  • DOI: 10.1038/nrmicro773

A human gut microbial gene catalogue established by metagenomic sequencing
journal, March 2010

  • Qin, Junjie; Li, Ruiqiang; Raes, Jeroen
  • Nature, Vol. 464, Issue 7285
  • DOI: 10.1038/nature08821

Function Discovery and Structural Characterization of a Methylphosphonate Esterase
journal, April 2015

Microbial carboxyl esterases: classification, properties and application in biocatalysis
journal, March 2002

Structures of bacterial kynurenine formamidase reveal a crowded binuclear zinc catalytic site primed to generate a potent nucleophile
journal, August 2014

  • Díaz-Sáez, Laura; Srikannathasan, Velupillai; Zoltner, Martin
  • Biochemical Journal, Vol. 462, Issue 3
  • DOI: 10.1042/BJ20140511

Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.
journal, April 1996

  • Herzberg, O.; Chen, C. C.; Kapadia, G.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 7
  • DOI: 10.1073/pnas.93.7.2652

Novel metal-binding site of Pseudomonas reinekei MT1 trans-dienelactone hydrolase
journal, December 2009

  • Marín, Macarena; Pieper, Dietmar H.
  • Biochemical and Biophysical Research Communications, Vol. 390, Issue 4
  • DOI: 10.1016/j.bbrc.2009.10.151

Exploring the new world of the genome with DNA microarrays
journal, January 1999

  • Brown, Patrick O.; Botstein, David
  • Nature Genetics, Vol. 21, Issue S1
  • DOI: 10.1038/4462

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008

ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions
journal, November 2012

  • Lenfant, Nicolas; Hotelier, Thierry; Velluet, Eric
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1154

Identification and characterization of novel poly(dl-lactic acid) depolymerases from metagenome
journal, July 2008

  • Mayumi, Daisuke; Akutsu-Shigeno, Yukie; Uchiyama, Hiroo
  • Applied Microbiology and Biotechnology, Vol. 79, Issue 5
  • DOI: 10.1007/s00253-008-1477-3

The Enzyme Function Initiative
journal, November 2011

  • Gerlt, John A.; Allen, Karen N.; Almo, Steven C.
  • Biochemistry, Vol. 50, Issue 46
  • DOI: 10.1021/bi201312u

Protein-protein interactions: methods for detection and analysis.
journal, January 1995

A novel family VIII carboxylesterase derived from a leachate metagenome library exhibits promiscuous β-lactamase activity on nitrocefin
journal, June 2009

  • Rashamuse, Konanani; Magomani, Victoria; Ronneburg, Tina
  • Applied Microbiology and Biotechnology, Vol. 83, Issue 3
  • DOI: 10.1007/s00253-009-1895-x

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016

  • Letunic, Ivica; Bork, Peer
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw290

Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014

  • Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1223

Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014

  • Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1223

Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes
journal, January 2010

  • Glass, E. M.; Wilkening, J.; Wilke, A.
  • Cold Spring Harbor Protocols, Vol. 2010, Issue 1
  • DOI: 10.1101/pdb.prot5368

Proteome-Scale Analysis of Biochemical Activity
journal, January 2006

  • Phizicky, Eric M.; Grayhack, Elizabeth J.
  • Critical Reviews in Biochemistry and Molecular Biology, Vol. 41, Issue 5
  • DOI: 10.1080/10409230600872872

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
journal, March 2007

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021

A new esterase EstD2 isolated from plant rhizosphere soil metagenome
journal, August 2010

  • Lee, Myung Hwan; Hong, Kyung Sik; Malhotra, Shweta
  • Applied Microbiology and Biotechnology, Vol. 88, Issue 5
  • DOI: 10.1007/s00253-010-2729-6

Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase
journal, October 2003

Protein arrays and microarrays
journal, February 2001

The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes
journal, September 2014

  • Tchigvintsev, Anatoli; Tran, Hai; Popovic, Ana
  • Applied Microbiology and Biotechnology, Vol. 99, Issue 5
  • DOI: 10.1007/s00253-014-6038-3

Environmental Genome Shotgun Sequencing of the Sargasso Sea
journal, April 2004

The α / β hydrolase fold
journal, January 1992

  • Ollis, David L.; Cheah, Eong; Cygler, Miroslaw
  • "Protein Engineering, Design and Selection", Vol. 5, Issue 3
  • DOI: 10.1093/protein/5.3.197

Cold-Adapted Enzymes
journal, June 2006

The Uncultured Microbial Majority
journal, October 2003

Proteome-Scale Analysis of Biochemical Activity
journal, January 2006

  • Phizicky, Eric M.; Grayhack, Elizabeth J.
  • Critical Reviews in Biochemistry and Molecular Biology, Vol. 41, Issue 5
  • DOI: 10.1080/10409230600872872

Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes
journal, January 2010

  • Glass, E. M.; Wilkening, J.; Wilke, A.
  • Cold Spring Harbor Protocols, Vol. 2010, Issue 1
  • DOI: 10.1101/pdb.prot5368

High diversity in DNA of soil bacteria.
journal, January 1990

Indication for a New Lipolytic Enzyme Family: Isolation and Characterization of Two Esterases from a Metagenomic Library
journal, January 2010

  • Bayer, Sally; Kunert, Anja; Ballschmiter, Meike
  • Journal of Molecular Microbiology and Biotechnology, Vol. 18, Issue 3
  • DOI: 10.1159/000315459

Structural proteomics of an archaeon
journal, October 2000

  • Edwards, Aled M.; Arrowsmith, Cheryl H.; Christendat, Dinesh
  • Nature Structural Biology, Vol. 7, Issue 10, p. 903-909
  • DOI: 10.1038/82823

The Enzyme Function Initiative
journal, November 2011

  • Gerlt, John A.; Allen, Karen N.; Almo, Steven C.
  • Biochemistry, Vol. 50, Issue 46
  • DOI: 10.1021/bi201312u

Mining genomes and ‘metagenomes’ for novel catalysts
journal, December 2005

Functional metagenomics for enzyme discovery: challenges to efficient screening
journal, December 2009

Metagenomics and the protein universe
journal, June 2011

Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends: Enzyme bioprospecting by metagenomics
journal, August 2015

  • Ferrer, Manuel; Martínez-Martínez, Mónica; Bargiela, Rafael
  • Microbial Biotechnology, Vol. 9, Issue 1
  • DOI: 10.1111/1751-7915.12309

Novel metal-binding site of Pseudomonas reinekei MT1 trans-dienelactone hydrolase
journal, December 2009

  • Marín, Macarena; Pieper, Dietmar H.
  • Biochemical and Biophysical Research Communications, Vol. 390, Issue 4
  • DOI: 10.1016/j.bbrc.2009.10.151

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
journal, January 2011

Function Discovery and Structural Characterization of a Methylphosphonate Esterase
journal, April 2015

SOLVE and RESOLVE: automated structure solution, density modification and model building
journal, November 2003

Automated MAD and MIR structure solution
journal, April 1999

  • Terwilliger, Thomas C.; Berendzen, Joel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 4
  • DOI: 10.1107/S0907444999000839

Cloning and Identification of a New Group Esterase (Est5S) from Noncultured Rumen Bacterium
journal, August 2012

High diversity in DNA of soil bacteria.
journal, January 1990

Protein-protein interactions: methods for detection and analysis.
journal, January 1995

Specific and sensitive plate assay for bacterial lipases.
journal, January 1987

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    A modified culture medium for improved isolation of marine vibrios
    journal, March 2019

    • Tagliavia, Marcello; Salamone, Monica; Bennici, Carmelo
    • MicrobiologyOpen, Vol. 8, Issue 9
    • DOI: 10.1002/mbo3.835

    Application of Cell-Free Protein Synthesis for Faster Biocatalyst Development
    journal, February 2019

    • Rolf, Jascha; Rosenthal, Katrin; Lütz, Stephan
    • Catalysts, Vol. 9, Issue 2
    • DOI: 10.3390/catal9020190

    Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines
    journal, November 2018

    • Coscolín, Cristina; Katzke, Nadine; García-Moyano, Antonio
    • Applied and Environmental Microbiology, Vol. 85, Issue 2
    • DOI: 10.1128/aem.02404-18

    A modified culture medium for improved isolation of marine vibrios
    journal, March 2019

    • Tagliavia, Marcello; Salamone, Monica; Bennici, Carmelo
    • MicrobiologyOpen, Vol. 8, Issue 9
    • DOI: 10.1002/mbo3.835

    Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines
    text, January 2019

    Application of the uridine auxotrophic host and synthetic nucleosides for a rapid selection of hydrolases from metagenomic libraries
    journal, October 2018

    • Urbelienė, Nina; Kutanovas, Simonas; Meškienė, Rita
    • Microbial Biotechnology, Vol. 12, Issue 1
    • DOI: 10.1111/1751-7915.13316

    A novel method for rapid and sensitive metagenomic activity screening
    journal, January 2018

    Insight Into Microbial Applications for the Biodegradation of Pyrethroid Insecticides
    journal, August 2019

    Microbial Metagenomics for Industrial and Environmental Bioprospecting: The Unknown Envoy
    book, January 2018

    Enzymes from Marine Polar Regions and Their Biotechnological Applications
    journal, September 2019

    • Bruno, Stefano; Coppola, Daniela; di Prisco, Guido
    • Marine Drugs, Vol. 17, Issue 10
    • DOI: 10.3390/md17100544

    A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri – Structural and Functional Insights
    journal, February 2020

    • Bollinger, Alexander; Thies, Stephan; Knieps-Grünhagen, Esther
    • Frontiers in Microbiology, Vol. 11
    • DOI: 10.3389/fmicb.2020.00114

    Application of cell-free protein synthesis for faster biocatalyst development
    text, January 2019

    • Rolf, Jascha; Rosenthal, Katrin; Lütz, Stephan
    • Technische Universität Dortmund
    • DOI: 10.17877/de290r-19948

    Enzymes from Marine Polar Regions and Their Biotechnological Applications
    journal, September 2019

    • Bruno, Stefano; Coppola, Daniela; di Prisco, Guido
    • Marine Drugs, Vol. 17, Issue 10
    • DOI: 10.3390/md17100544

    A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri – Structural and Functional Insights
    text, January 2020

    • Bollinger, Alexander; Thies, Stephan; Knieps-Grünhagen, Esther
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-03228

    Agar plate‐based screening methods for the identification of polyester hydrolysis by Pseudomonas species
    journal, January 2020

    • Molitor, Rebecka; Bollinger, Alexander; Kubicki, Sonja
    • Microbial Biotechnology, Vol. 13, Issue 1
    • DOI: 10.1111/1751-7915.13418

    Metagenomics: novel enzymes from non-culturable microbes
    journal, October 2017

    • Berini, Francesca; Casciello, Carmine; Marcone, Giorgia Letizia
    • FEMS Microbiology Letters, Vol. 364, Issue 21
    • DOI: 10.1093/femsle/fnx211

    Decoding the ocean's microbiological secrets for marine enzyme biodiscovery
    journal, December 2018

    • Ferrer, Manuel; Méndez-García, Celia; Bargiela, Rafael
    • FEMS Microbiology Letters, Vol. 366, Issue 1
    • DOI: 10.1093/femsle/fny285
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: