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

Title: Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study

Abstract

Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass, is discovered to promote the degradation of Azo dye by white-rot fungus Irpex lacteus CD2 in the lignin/dye/fungus system. Shotgun proteomics technique was used to understand degradation mechanism at the protein level for the lignin/dye/fungus system. Our proteomics study can identify about two thousand proteins (one third of the predicted white-rot fungal proteome) in a single experiment, as one of the most powerful proteomics platforms to study the fungal system to date. The study shows a significant enrichment of oxidoreduction functional category under the dye/lignin combined treatment. An in vitro validation is performed and supports our hypothesis that the synergy of Fenton reaction and manganese peroxidase might play an important role in DR5B dye degradation. The results could guide the development of effective bioremediation strategies and efficient lignocellulosic biomass conversion.

Authors:
 [1];  [2];  [3];  [2];  [4];  [3];  [3];  [4];  [3];  [5]
  1. Huazhong Univ. of Science and Technology, Wuhan (China). School of Life Science and Technology; Texas A & M Univ., College Station, TX (United States). Dept. of Veterinary Pathology
  2. Huazhong Univ. of Science and Technology, Wuhan (China). School of Life Science and Technology; Texas A & M Univ., College Station, TX (United States). Synthetic and Systems Biology Innovation Hub. Dept. of Plant Pathology and Microbiology
  3. Texas A & M Univ., College Station, TX (United States). Synthetic and Systems Biology Innovation Hub. Dept. of Plant Pathology and Microbiology
  4. Huazhong Univ. of Science and Technology, Wuhan (China). School of Life Science and Technology
  5. Texas A & M Univ., College Station, TX (United States). Dept. of Veterinary Pathology. Office of Texas State Chemist
Publication Date:
Research Org.:
Texas A & M Univ., College Station, TX (United States); Huazhong Univ. of Science and Technology, Wuhan (China)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B); National Natural Science Foundation of China (NNSFC); National High-tech Research and Development Program of China; Major State Basic Research Development Program of China
OSTI Identifier:
1425151
Grant/Contract Number:  
[EE0006112; EE0007104; 31170104; 2012AA101805; 2014CB138301]
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; proteomics; water microbiology

Citation Formats

Sun, Su, Xie, Shangxian, Cheng, Yanbing, Yu, Hongbo, Zhao, Honglu, Li, Muzi, Li, Xiaotong, Zhang, Xiaoyu, Yuan, Joshua S., and Dai, Susie Y. Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study. United States: N. p., 2017. Web. doi:10.1038/s41598-017-10132-4.
Sun, Su, Xie, Shangxian, Cheng, Yanbing, Yu, Hongbo, Zhao, Honglu, Li, Muzi, Li, Xiaotong, Zhang, Xiaoyu, Yuan, Joshua S., & Dai, Susie Y. Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study. United States. doi:10.1038/s41598-017-10132-4.
Sun, Su, Xie, Shangxian, Cheng, Yanbing, Yu, Hongbo, Zhao, Honglu, Li, Muzi, Li, Xiaotong, Zhang, Xiaoyu, Yuan, Joshua S., and Dai, Susie Y. Tue . "Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study". United States. doi:10.1038/s41598-017-10132-4. https://www.osti.gov/servlets/purl/1425151.
@article{osti_1425151,
title = {Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study},
author = {Sun, Su and Xie, Shangxian and Cheng, Yanbing and Yu, Hongbo and Zhao, Honglu and Li, Muzi and Li, Xiaotong and Zhang, Xiaoyu and Yuan, Joshua S. and Dai, Susie Y.},
abstractNote = {Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass, is discovered to promote the degradation of Azo dye by white-rot fungus Irpex lacteus CD2 in the lignin/dye/fungus system. Shotgun proteomics technique was used to understand degradation mechanism at the protein level for the lignin/dye/fungus system. Our proteomics study can identify about two thousand proteins (one third of the predicted white-rot fungal proteome) in a single experiment, as one of the most powerful proteomics platforms to study the fungal system to date. The study shows a significant enrichment of oxidoreduction functional category under the dye/lignin combined treatment. An in vitro validation is performed and supports our hypothesis that the synergy of Fenton reaction and manganese peroxidase might play an important role in DR5B dye degradation. The results could guide the development of effective bioremediation strategies and efficient lignocellulosic biomass conversion.},
doi = {10.1038/s41598-017-10132-4},
journal = {Scientific Reports},
number = ,
volume = [7],
place = {United States},
year = {2017},
month = {9}
}

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

Citation Metrics:
Cited by: 3 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Methodologies and Perspectives of Proteomics Applied to Filamentous Fungi: From Sample Preparation to Secretome Analysis
journal, March 2015

  • Bianco, Linda; Perrotta, Gaetano
  • International Journal of Molecular Sciences, Vol. 16, Issue 12
  • DOI: 10.3390/ijms16035803

Induction of Extracellular Hydroxyl Radical Production by White-Rot Fungi through Quinone Redox Cycling
journal, April 2009

  • Gomez-Toribio, V.; Garcia-Martin, A. B.; Martinez, M. J.
  • Applied and Environmental Microbiology, Vol. 75, Issue 12
  • DOI: 10.1128/AEM.02137-08

Carcinogenicity of azo colorants: influence of solubility and bioavailability
journal, June 2004


Comparative Transcriptome and Secretome Analysis of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium
journal, April 2010

  • Vanden Wymelenberg, A.; Gaskell, J.; Mozuch, M.
  • Applied and Environmental Microbiology, Vol. 76, Issue 11
  • DOI: 10.1128/AEM.00058-10

The impact of proteomics on the understanding of functions and biogenesis of fungal extracellular vesicles
journal, January 2014


Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation
journal, July 2013

  • Yakovlev, Igor A.; Hietala, Ari M.; Courty, Pierre-Emmanuel
  • Fungal Genetics and Biology, Vol. 56
  • DOI: 10.1016/j.fgb.2013.04.011

Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel—from systems biology to synthetic design
journal, June 2014


Cytoscape 2.8: new features for data integration and network visualization
journal, December 2010


Identification of a Serine Hydrolase Which Cleaves the Alicyclic Ring of Tetralin
journal, October 2000


Simultaneous conversion of all cell wall components by an oleaginous fungus without chemi-physical pretreatment
journal, January 2015

  • Xie, Shangxian; Qin, Xing; Cheng, Yanbing
  • Green Chemistry, Vol. 17, Issue 3
  • DOI: 10.1039/C4GC01529K

Plant Protein-Protein Interaction Network and Interactome
journal, March 2010


Next-generation proteomics: towards an integrative view of proteome dynamics
journal, December 2012

  • Altelaar, A. F. Maarten; Munoz, Javier; Heck, Albert J. R.
  • Nature Reviews Genetics, Vol. 14, Issue 1
  • DOI: 10.1038/nrg3356

Analyzing Shotgun Proteomic Data with PatternLab for Proteomics
journal, June 2010

  • Carvalho, Paulo C.; Yates III, John R.; Barbosa, Valmir C.
  • Current Protocols in Bioinformatics, Vol. 30, Issue 1
  • DOI: 10.1002/0471250953.bi1313s30

White-rot fungi and their enzymes for the treatment of industrial dye effluents
journal, December 2003


WGCNA: an R package for weighted correlation network analysis
journal, December 2008


Large-scale analysis of the yeast proteome by multidimensional protein identification technology
journal, March 2001

  • Washburn, Michael P.; Wolters, Dirk; Yates, John R.
  • Nature Biotechnology, Vol. 19, Issue 3
  • DOI: 10.1038/85686

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0
journal, December 2015

  • Carvalho, Paulo C.; Lima, Diogo B.; Leprevost, Felipe V.
  • Nature Protocols, Vol. 11, Issue 1
  • DOI: 10.1038/nprot.2015.133

Genomic and molecular mechanisms for efficient biodegradation of aromatic dye
journal, January 2016


Advances in fungal proteomics
journal, July 2007


Influence of culture parameters on lignin metabolism byPhanerochaete chrysosporium
journal, June 1978

  • Kirk, T. K.; Schultz, E.; Connors, W. J.
  • Archives of Microbiology, Vol. 117, Issue 3
  • DOI: 10.1007/BF00738547

SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Fungal proteomics: from identification to function: Fungal proteomics
journal, May 2011


Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis
journal, March 2012

  • Fernandez-Fueyo, E.; Ruiz-Duenas, F. J.; Ferreira, P.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 14, p. 5458-5463
  • DOI: 10.1073/pnas.1119912109

Bladder cancer among workers in the textile industry: Results of a spanish case-control study
journal, January 1988

  • Gonzales, Carlos A.; Riboli, Elio; Lopez-Abente, Gonzalo
  • American Journal of Industrial Medicine, Vol. 14, Issue 6
  • DOI: 10.1002/ajim.4700140607

Plant systems biology comes of age
journal, April 2008


Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains
journal, January 2014


Elucidating the fungal stress response by proteomics
journal, January 2014


Differential proteomic analysis of the secretome of Irpex lacteus and other white-rot fungi during wheat straw pretreatment
journal, January 2013

  • Salvachúa, Davinia; Martínez, Angel T.; Tien, Ming
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-115

Proteomic and Metabolomic Analyses of the White-Rot Fungus Phanerochaete chrysosporium Exposed to Exogenous Benzoic Acid
journal, June 2008

  • Matsuzaki, Fumiko; Shimizu, Motoyuki; Wariishi, Hiroyuki
  • Journal of Proteome Research, Vol. 7, Issue 6
  • DOI: 10.1021/pr700617s

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion
journal, February 2009

  • Martinez, Diego; Challacombe, Jean; Morgenstern, Ingo
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 6
  • DOI: 10.1073/pnas.0809575106

Application of an Improved Proteomics Method for Abundant Protein Cleanup: Molecular and Genomic Mechanisms Study in Plant Defense
journal, August 2013

  • Zhang, Yixiang; Gao, Peng; Xing, Zhuo
  • Molecular & Cellular Proteomics, Vol. 12, Issue 11
  • DOI: 10.1074/mcp.M112.025213

Applying mass spectrometry-based proteomics to genetics, genomics and network biology
journal, September 2009

  • Gstaiger, Matthias; Aebersold, Ruedi
  • Nature Reviews Genetics, Vol. 10, Issue 9
  • DOI: 10.1038/nrg2633

Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics
journal, December 2010

  • Chourey, Karuna; Jansson, Janet; VerBerkmoes, Nathan
  • Journal of Proteome Research, Vol. 9, Issue 12
  • DOI: 10.1021/pr100787q

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications
journal, August 2009


ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity
journal, November 2015


Proteomics of filamentous fungi
journal, September 2007


Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
journal, May 2004

  • Martinez, Diego; Larrondo, Luis F.; Putnam, Nik
  • Nature Biotechnology, Vol. 22, Issue 6
  • DOI: 10.1038/nbt967

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
journal, December 2008

  • Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A.
  • Nature Protocols, Vol. 4, Issue 1
  • DOI: 10.1038/nprot.2008.211

Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa
journal, December 2009

  • Tian, Chaoguang; Beeson, William T.; Iavarone, Anthony T.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 52
  • DOI: 10.1073/pnas.0906810106