skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization

Abstract

Background: Metagenomics approaches provide access to environmental genetic diversity for biotechnology applications, enabling the discovery of new enzymes and pathways for numerous catalytic processes. Discovery of new glycoside hydrolases with improved biocatalytic properties for the efficient conversion of lignocellulosic material to biofuels is a critical challenge in the development of economically viable routes from biomass to fuels and chemicals.Results: Twenty-two putative ORFs (open reading frames) were identified from a switchgrass-adapted compost community based on sequence homology to related gene families. These ORFs were expressed in E. coli and assayed for predicted activities. Seven of the ORFs were demonstrated to encode active enzymes, encompassing five classes of hemicellulases. Four enzymes were over expressed in vivo, purified to homogeneity and subjected to detailed biochemical characterization. Their pH optima ranged between 5.5 - 7.5 and they exhibit moderate thermostability up to ~60-70°C.Conclusions: Seven active enzymes were identified from this set of ORFs comprising five different hemicellulose activities. These enzymes have been shown to have useful properties, such as moderate thermal stability and broad pH optima, and may serve as the starting points for future protein engineering towards the goal of developing efficient enzyme cocktails for biomass degradation under diverse process conditions.

Authors:
 [1];  [2];  [3];  [1];  [4];  [5]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  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. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), 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). Biological Systems Science Division
OSTI Identifier:
1511338
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
BMC Biotechnology (Online)
Additional Journal Information:
Journal Name: BMC Biotechnology (Online); Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1472-6750
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Glycoside Hydrolase; Acetyl Esterase; Autoinduction Medium; Wheat Arabinoxylan; Endoxylanase Activity

Citation Formats

Dougherty, Michael J., D’haeseleer, Patrik, Hazen, Terry C., Simmons, Blake A., Adams, Paul D., and Hadi, Masood Z. Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization. United States: N. p., 2012. Web. doi:10.1186/1472-6750-12-38.
Dougherty, Michael J., D’haeseleer, Patrik, Hazen, Terry C., Simmons, Blake A., Adams, Paul D., & Hadi, Masood Z. Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization. United States. doi:10.1186/1472-6750-12-38.
Dougherty, Michael J., D’haeseleer, Patrik, Hazen, Terry C., Simmons, Blake A., Adams, Paul D., and Hadi, Masood Z. Tue . "Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization". United States. doi:10.1186/1472-6750-12-38. https://www.osti.gov/servlets/purl/1511338.
@article{osti_1511338,
title = {Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization},
author = {Dougherty, Michael J. and D’haeseleer, Patrik and Hazen, Terry C. and Simmons, Blake A. and Adams, Paul D. and Hadi, Masood Z.},
abstractNote = {Background: Metagenomics approaches provide access to environmental genetic diversity for biotechnology applications, enabling the discovery of new enzymes and pathways for numerous catalytic processes. Discovery of new glycoside hydrolases with improved biocatalytic properties for the efficient conversion of lignocellulosic material to biofuels is a critical challenge in the development of economically viable routes from biomass to fuels and chemicals.Results: Twenty-two putative ORFs (open reading frames) were identified from a switchgrass-adapted compost community based on sequence homology to related gene families. These ORFs were expressed in E. coli and assayed for predicted activities. Seven of the ORFs were demonstrated to encode active enzymes, encompassing five classes of hemicellulases. Four enzymes were over expressed in vivo, purified to homogeneity and subjected to detailed biochemical characterization. Their pH optima ranged between 5.5 - 7.5 and they exhibit moderate thermostability up to ~60-70°C.Conclusions: Seven active enzymes were identified from this set of ORFs comprising five different hemicellulose activities. These enzymes have been shown to have useful properties, such as moderate thermal stability and broad pH optima, and may serve as the starting points for future protein engineering towards the goal of developing efficient enzyme cocktails for biomass degradation under diverse process conditions.},
doi = {10.1186/1472-6750-12-38},
journal = {BMC Biotechnology (Online)},
number = 1,
volume = 12,
place = {United States},
year = {2012},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 30 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: Diverse CAZy-family genes members were identified in the metagenome from switchgrass compost. The putative reconstructed genes are predicted to fall into 12 different CAZy families. The most abundant families are GH10, GH43, and GH51. Homology-based protein structure predictions were generated using AS2TS (proteinmodel.org). All members were expressed inmore » E coli and screened for expression and activity. Colored structures were expressed and characterized biochemically while the black and white structures were not.« less

Save / Share:

Works referenced in this record:

Diversity of Glycosyl Hydrolases from Cellulose-Depleting Communities Enriched from Casts of Two Earthworm Species
journal, July 2010

  • Beloqui, A.; Nechitaylo, T. Y.; Lopez-Cortes, N.
  • Applied and Environmental Microbiology, Vol. 76, Issue 17
  • DOI: 10.1128/AEM.00902-10

AS2TS system for protein structure modeling and analysis
journal, July 2005

  • Zemla, A.; Zhou, C. E.; Slezak, T.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki457

Advances in Recovery of Novel Biocatalysts from Metagenomes
journal, January 2009

  • Steele, Helen L.; Jaeger, Karl-Erich; Daniel, Rolf
  • Journal of Molecular Microbiology and Biotechnology, Vol. 16, Issue 1-2
  • DOI: 10.1159/000142892

Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass
journal, July 2011

  • Gladden, John M.; Allgaier, Martin; Miller, Christopher S.
  • Applied and Environmental Microbiology, Vol. 77, Issue 16, p. 5804-5812
  • DOI: 10.1128/AEM.00032-11

Metagenomic era for biocatalyst identification
journal, December 2010

  • Fernández-Arrojo, Lucía; Guazzaroni, María-Eugenia; López-Cortés, Nieves
  • Current Opinion in Biotechnology, Vol. 21, Issue 6
  • DOI: 10.1016/j.copbio.2010.09.006

Bioprospecting metagenomes: glycosyl hydrolases for converting biomass
journal, January 2009

  • Li, Luen-Luen; McCorkle, Sean R.; Monchy, Sebastien
  • Biotechnology for Biofuels, Vol. 2, Issue 1
  • DOI: 10.1186/1754-6834-2-10

Protein engineering in designing tailored enzymes and microorganisms for biofuels production
journal, August 2009


Exploring microbial diversity for biotechnology: the way forward
journal, March 2010


Xylanases, xylanase families and extremophilic xylanases
journal, January 2005


Biochemical characterization of a novel dual-function arabinofuranosidase/xylosidase isolated from a compost starter mixture
journal, September 2008

  • Wagschal, Kurt; Heng, Chamroeun; Lee, Charles C.
  • Applied Microbiology and Biotechnology, Vol. 81, Issue 5
  • DOI: 10.1007/s00253-008-1662-4

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

  • Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn663

Metagenomic gene discovery: How far have we moved into novel sequence space?
journal, December 2009

  • Tuffin, Marla; Anderson, Dominique; Heath, Cal
  • Biotechnology Journal, Vol. 4, Issue 12
  • DOI: 10.1002/biot.200900235

Protein production by auto-induction in high-density shaking cultures
journal, May 2005


Metagenomics and the protein universe
journal, June 2011


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


Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
journal, January 2010


Cellulosic Biofuels
journal, June 2009


Recent progress and new challenges in metagenomics for biotechnology
journal, May 2010


Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar
journal, March 1959


    Works referencing / citing this record:

    Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome
    journal, April 2019

    • Fortune, Brent; Mhlongo, Sizwe; van Zyl, Leonardo Joaquim
    • BMC Biotechnology, Vol. 19, Issue 1
    • DOI: 10.1186/s12896-019-0510-1

    Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library
    journal, June 2017


    Screening, identification, and characterization of a novel saccharide-stimulated β-glycosidase from a soil metagenomic library
    journal, August 2016

    • Matsuzawa, Tomohiko; Yaoi, Katsuro
    • Applied Microbiology and Biotechnology, Vol. 101, Issue 2
    • DOI: 10.1007/s00253-016-7803-2

    Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome
    journal, April 2019

    • Fortune, Brent; Mhlongo, Sizwe; van Zyl, Leonardo Joaquim
    • BMC Biotechnology, Vol. 19, Issue 1
    • DOI: 10.1186/s12896-019-0510-1

    Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library
    journal, June 2017


      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.