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

Title: Novosphingobium aromaticivorans uses a Nu-class glutathione S -transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

Abstract

As a major component of plant cells walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione-S-transferase NaGST Nu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans. We solved the crystal structure of NaGST Nu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr 51, Tyr 166, and Tyr 224) were found to be critical for the lyasemore » reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione-S-transferases.« less

Authors:
 [1];  [2];  [1];  [1];  [3];  [1];  [2];  [4];  [5];  [6];  [7];  [8]
  1. Univ. of Wisconsin, Madison, WI (United States). Wisconsin Energy Institute and Department of Energy Great Lakes Bioenergy Research Center
  2. Univ. of Wisconsin, Madison, WI (United States). Department of Energy Great Lakes Bioenergy Research Center and Department of Biochemistry
  3. Univ. of Wisconsin, Madison, WI (United States). Department of Chemistry and Genome Center of Wisconsin
  4. Univ. of Wisconsin, Madison, WI (United States). Department of Chemistry
  5. Univ. of Wisconsin, Madison, WI (United States). Wisconsin Energy Institute, Department of Energy Great Lakes Bioenergy Research Center and Department of Biochemistry
  6. Univ. of Wisconsin, Madison, WI (United States). Wisconsin Energy Institute, Department of Energy Great Lakes Bioenergy Research Center and Civil and Environmental Engineering
  7. Univ. of Wisconsin, Madison, WI (United States). Wisconsin Energy Institute, Department of Energy Great Lakes Bioenergy Research Center, Department of Chemistry, Genome Center of Wisconsin and Department of Biomolecular Chemistry
  8. Univ. of Wisconsin, Madison, WI (United States). Wisconsin Energy Institute, Department of Energy Great Lakes Bioenergy Research Center and Department of Bacteriology
Publication Date:
Research Org.:
Great Lakes Bioenergy Research Center, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Contributing Org.:
Advanced Photon Source at Argonne National Laboratory
OSTI Identifier:
1459440
Grant/Contract Number:  
SC0018409; FC02-07ER64494; AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 293; Journal Issue: 14; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Glutathione-S-transferases; Nu-class; β-aryl ether; deglutathionylation; Novosphingobium aromaticivorans; bacterial metabolism; enzyme mechanism; enzyme structure; lignin degradation; Escherichia coli

Citation Formats

Kontur, Wayne S., Bingman, Craig A., Olmsted, Charles N., Wassarman, Douglas R., Ulbrich, Arne, Gall, Daniel L., Smith, Robert W., Yusko, Larissa M., Fox, Brian G., Noguera, Daniel R., Coon, Joshua J., and Donohue, Timothy J. Novosphingobium aromaticivorans uses a Nu-class glutathione S -transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin. United States: N. p., 2018. Web. doi:10.1074/jbc.RA117.001268.
Kontur, Wayne S., Bingman, Craig A., Olmsted, Charles N., Wassarman, Douglas R., Ulbrich, Arne, Gall, Daniel L., Smith, Robert W., Yusko, Larissa M., Fox, Brian G., Noguera, Daniel R., Coon, Joshua J., & Donohue, Timothy J. Novosphingobium aromaticivorans uses a Nu-class glutathione S -transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin. United States. doi:10.1074/jbc.RA117.001268.
Kontur, Wayne S., Bingman, Craig A., Olmsted, Charles N., Wassarman, Douglas R., Ulbrich, Arne, Gall, Daniel L., Smith, Robert W., Yusko, Larissa M., Fox, Brian G., Noguera, Daniel R., Coon, Joshua J., and Donohue, Timothy J. Thu . "Novosphingobium aromaticivorans uses a Nu-class glutathione S -transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin". United States. doi:10.1074/jbc.RA117.001268. https://www.osti.gov/servlets/purl/1459440.
@article{osti_1459440,
title = {Novosphingobium aromaticivorans uses a Nu-class glutathione S -transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin},
author = {Kontur, Wayne S. and Bingman, Craig A. and Olmsted, Charles N. and Wassarman, Douglas R. and Ulbrich, Arne and Gall, Daniel L. and Smith, Robert W. and Yusko, Larissa M. and Fox, Brian G. and Noguera, Daniel R. and Coon, Joshua J. and Donohue, Timothy J.},
abstractNote = {As a major component of plant cells walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione-S-transferase NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans. We solved the crystal structure of NaGSTNu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr51, Tyr166, and Tyr224) were found to be critical for the lyase reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione-S-transferases.},
doi = {10.1074/jbc.RA117.001268},
journal = {Journal of Biological Chemistry},
issn = {0021-9258},
number = 14,
volume = 293,
place = {United States},
year = {2018},
month = {2}
}

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

Citation Metrics:
Cited by: 5 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6
journal, March 2016

  • Pereira, Jose Henrique; Heins, Richard A.; Gall, Daniel L.
  • Journal of Biological Chemistry, Vol. 291, Issue 19
  • DOI: 10.1074/jbc.M115.700427

A Group of Sequence-Related Sphingomonad Enzymes Catalyzes Cleavage of β-Aryl Ether Linkages in Lignin β-Guaiacyl and β-Syringyl Ether Dimers
journal, October 2014

  • Gall, Daniel L.; Ralph, John; Donohue, Timothy J.
  • Environmental Science & Technology, Vol. 48, Issue 20
  • DOI: 10.1021/es503886d

Identification of Genes Required for Recycling Reducing Power during Photosynthetic Growth
journal, July 2005


EIGER detector: application in macromolecular crystallography
journal, August 2016

  • Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 9
  • DOI: 10.1107/S2059798316012304

Aromatic rings act as hydrogen bond acceptors
journal, June 1988


Detection and localization of a new enzyme catalyzing the β-aryl ether cleavage in the soil bacterium ( Pseudomonas paucimobilis SYK-6)
journal, June 1989


The effects of mutating Tyr9 and Arg15 on the structure, stability, conformational dynamics and mechanism of GSTA3-3
journal, May 2017


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

The Marine Isolate Novosphingobium sp. PP1Y Shows Specific Adaptation to Use the Aromatic Fraction of Fuels as the Sole Carbon and Energy Source
journal, January 2011

  • Notomista, Eugenio; Pennacchio, Francesca; Cafaro, Valeria
  • Microbial Ecology, Vol. 61, Issue 3
  • DOI: 10.1007/s00248-010-9786-3

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

Biochemical transformation of lignin for deriving valued commodities from lignocellulose
journal, June 2017


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


Atypical features of a Ure2p glutathione transferase from Phanerochaete chrysosporium
journal, May 2013


Structure, Catalytic Mechanism, and Evolution of the Glutathione Transferases
journal, January 1997

  • Armstrong, Richard N.
  • Chemical Research in Toxicology, Vol. 10, Issue 1
  • DOI: 10.1021/tx960072x

Characterization of the Third Glutathione S -Transferase Gene Involved in Enantioselective Cleavage of the β-Aryl Ether by Sphingobium sp. Strain SYK-6
journal, December 2011

  • Tanamura, Kazuyuki; Abe, Tomokuni; Kamimura, Naofumi
  • Bioscience, Biotechnology, and Biochemistry, Vol. 75, Issue 12
  • DOI: 10.1271/bbb.110525

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

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

Structure and Function of YghU, a Nu-Class Glutathione Transferase Related to YfcG from Escherichia coli
journal, February 2011

  • Stourman, Nina V.; Branch, Megan C.; Schaab, Matthew R.
  • Biochemistry, Vol. 50, Issue 7
  • DOI: 10.1021/bi101861a

The Aerobic Pseudomonads a Taxonomic Study
journal, May 1966

  • Stanier, R. Y.; Palleroni, N. J.; Doudoroff, M.
  • Journal of General Microbiology, Vol. 43, Issue 2
  • DOI: 10.1099/00221287-43-2-159

Identification of Three Alcohol Dehydrogenase Genes Involved in the Stereospecific Catabolism of Arylglycerol- -Aryl Ether by Sphingobium sp. Strain SYK-6
journal, June 2009

  • Sato, Y.; Moriuchi, H.; Hishiyama, S.
  • Applied and Environmental Microbiology, Vol. 75, Issue 16
  • DOI: 10.1128/AEM.00880-09

Evolutionary divergence of Ure2pA glutathione transferases in wood degrading fungi
journal, October 2015


A superior host strain for the over-expression of cloned genes using the T7 promoter based vectors
journal, January 1995

  • Doherty, Aidan J.; Ashford, Stephen R.; Brannigan, James A.
  • Nucleic Acids Research, Vol. 23, Issue 11
  • DOI: 10.1093/nar/23.11.2074

Combination of six enzymes of a marine Novosphingobium converts the stereoisomers of β-O-4 lignin model dimers into the respective monomers
journal, October 2015

  • Ohta, Yukari; Nishi, Shinro; Hasegawa, Ryoichi
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep15105

Large-Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere
journal, April 2014


Kinetic studies of pigment synthesis by non-sulfur purple bacteria
journal, February 1957

  • Cohen-Bazire, Germaine; Sistrom, W. R.; Stanier, R. Y.
  • Journal of Cellular and Comparative Physiology, Vol. 49, Issue 1
  • DOI: 10.1002/jcp.1030490104

Lignin chemistry?past, present and future
journal, January 1977


Three Distinct-Type Glutathione S-Transferases from Escherichia coli Important for Defense against Oxidative Stress
journal, November 2006

  • Kanai, Takuya; Takahashi, Kenji; Inoue, Hideshi
  • The Journal of Biochemistry, Vol. 140, Issue 5
  • DOI: 10.1093/jb/mvj199

The Kinetics of the Synthesis of Photopigments in Rhodopseudomonas spheroides
journal, September 1962


Correction to Analysis of the Structure and Function of YfcG from Escherichia coli Reveals an Efficient and Unique Disulfide Bond Reductase
journal, December 2010

  • Wadington, Megan C.; Ladner, Jane E.; Stourman, Nina V.
  • Biochemistry, Vol. 49, Issue 50
  • DOI: 10.1021/bi101851x

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Description of Sphingomonas xenophaga sp. nov. for strains BN6(T) and N,N which degrade xenobiotic aromatic compounds
journal, January 2000

  • Stolz, A.; Schmidt-Maag, C.; Denner, E.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 1
  • DOI: 10.1099/00207713-50-1-35

Roles of the Enantioselective Glutathione S-Transferases in Cleavage of  -Aryl Ether
journal, March 2003


Stereochemical Features of Glutathione-dependent Enzymes in the Sphingobium sp. Strain SYK-6 β-Aryl Etherase Pathway
journal, February 2014

  • Gall, Daniel L.; Kim, Hoon; Lu, Fachuang
  • Journal of Biological Chemistry, Vol. 289, Issue 12
  • DOI: 10.1074/jbc.M113.536250

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Improvement of molecular-replacement models with Sculptor
journal, March 2011

  • Bunkóczi, Gábor; Read, Randy J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910051218

Analysis of the Structure and Function of YfcG from Escherichia coli Reveals an Efficient and Unique Disulfide Bond Reductase
journal, July 2009

  • Wadington, Megan C.; Ladner, Jane E.; Stourman, Nina V.
  • Biochemistry, Vol. 48, Issue 28
  • DOI: 10.1021/bi9008825

    Works referencing / citing this record:

    Internalization and accumulation of model lignin breakdown products in bacteria and fungi
    journal, July 2019

    • Barnhart-Dailey, Meghan C.; Ye, Dongmei; Hayes, Dulce C.
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1494-8

    Internalization and accumulation of model lignin breakdown products in bacteria and fungi
    journal, July 2019

    • Barnhart-Dailey, Meghan C.; Ye, Dongmei; Hayes, Dulce C.
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1494-8