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

Title: Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling

Abstract

Here, the development of renewable biofuels is a global priority, but success will require novel technologies that greatly improve our understanding of microbial systems biology. An approach with great promise in enabling functional characterization of microbes is activity-based protein profiling (ABPP), which employs chemical probes to directly measure enzyme function in discrete enzyme classes in vivo and/or in vitro, thereby facilitating the rapid discovery of new biocatalysts and enabling much improved biofuel production platforms. We review general design strategies in ABPP, and highlight recent advances that are or could be pivotal to biofuels processes including applications of ABPP to cellulosic bioethanol, biodiesel, and phototrophic production of hydrocarbons. We also examine the key challenges and opportunities of ABPP in renewable biofuels research. The integration of ABPP with molecular and systems biology approaches will shed new insight on the catalytic and regulatory mechanisms of functional enzymes and their synergistic effects in the field of biofuels production.

Authors:
 [1];  [2];  [2];  [2];  [2];  [2]
  1. Beijing Univ. of Chemical Technology, Beijing (China)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1243254
Report Number(s):
PNNL-SA-107650
Journal ID: ISSN 1754-6834; 48680; 48672; KP1601010
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; activity-based protein profiling (ABPP); cellulosic bioethanol; biodiesel; protein redox; proteomics; environmental molecular sciences laboratory

Citation Formats

Liu, Yun, Fredrickson, James K., Sadler, Natalie C., Nandhikonda, Premchendar, Smith, Richard D., and Wright, Aaron T. Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling. United States: N. p., 2015. Web. doi:10.1186/s13068-015-0343-7.
Liu, Yun, Fredrickson, James K., Sadler, Natalie C., Nandhikonda, Premchendar, Smith, Richard D., & Wright, Aaron T. Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling. United States. doi:10.1186/s13068-015-0343-7.
Liu, Yun, Fredrickson, James K., Sadler, Natalie C., Nandhikonda, Premchendar, Smith, Richard D., and Wright, Aaron T. Fri . "Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling". United States. doi:10.1186/s13068-015-0343-7. https://www.osti.gov/servlets/purl/1243254.
@article{osti_1243254,
title = {Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling},
author = {Liu, Yun and Fredrickson, James K. and Sadler, Natalie C. and Nandhikonda, Premchendar and Smith, Richard D. and Wright, Aaron T.},
abstractNote = {Here, the development of renewable biofuels is a global priority, but success will require novel technologies that greatly improve our understanding of microbial systems biology. An approach with great promise in enabling functional characterization of microbes is activity-based protein profiling (ABPP), which employs chemical probes to directly measure enzyme function in discrete enzyme classes in vivo and/or in vitro, thereby facilitating the rapid discovery of new biocatalysts and enabling much improved biofuel production platforms. We review general design strategies in ABPP, and highlight recent advances that are or could be pivotal to biofuels processes including applications of ABPP to cellulosic bioethanol, biodiesel, and phototrophic production of hydrocarbons. We also examine the key challenges and opportunities of ABPP in renewable biofuels research. The integration of ABPP with molecular and systems biology approaches will shed new insight on the catalytic and regulatory mechanisms of functional enzymes and their synergistic effects in the field of biofuels production.},
doi = {10.1186/s13068-015-0343-7},
journal = {Biotechnology for Biofuels},
number = ,
volume = 8,
place = {United States},
year = {2015},
month = {9}
}

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

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

The Path Forward for Biofuels and Biomaterials
journal, January 2006

  • Ragauskas, Arthur J.; Williams, Charlotte K.; Davison, Brian H.
  • Science, Vol. 311, Issue 5760, p. 484-489
  • DOI: 10.1126/science.1114736

Genomics of cellulosic biofuels
journal, August 2008


Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

Activity-based protein profiling of microbes
journal, February 2015


Current Developments in Activity-Based Protein Profiling
journal, June 2014

  • Willems, Lianne I.; Overkleeft, Herman S.; van Kasteren, Sander I.
  • Bioconjugate Chemistry, Vol. 25, Issue 7
  • DOI: 10.1021/bc500208y

Activity-Based Protein Profiling: From Enzyme Chemistry to Proteomic Chemistry
journal, June 2008


Chemical ‘omics’ approaches for understanding protein cysteine oxidation in biology
journal, February 2011


Small-molecule probes elucidate global enzyme activity in a proteomic context
journal, March 2014


Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)
journal, January 2015

  • Wang, Jigang; Zhang, Chong-Jing; Zhang, Jianbin
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep07896

Activity-based proteomic and metabolomic approaches for understanding metabolism
journal, August 2014


Activity-based protein profiling for biochemical pathway discovery in cancer
journal, August 2010

  • Nomura, Daniel K.; Dix, Melissa M.; Cravatt, Benjamin F.
  • Nature Reviews Cancer, Vol. 10, Issue 9
  • DOI: 10.1038/nrc2901

Pretubulysin derived probes as novel tools for monitoring the microtubule network via activity-based protein profiling and fluorescence microscopy
journal, January 2012

  • Eirich, Jürgen; Burkhart, Jens L.; Ullrich, Angelika
  • Molecular BioSystems, Vol. 8, Issue 8
  • DOI: 10.1039/c2mb25144b

Organelle-Specific Activity-Based Protein Profiling in Living Cells
journal, February 2014

  • Wiedner, Susan D.; Anderson, Lindsey N.; Sadler, Natalie C.
  • Angewandte Chemie International Edition, Vol. 53, Issue 11
  • DOI: 10.1002/anie.201309135

Functional Imaging of Legumain in Cancer Using a New Quenched Activity-Based Probe
journal, December 2012

  • Edgington, Laura E.; Verdoes, Martijn; Ortega, Alberto
  • Journal of the American Chemical Society, Vol. 135, Issue 1
  • DOI: 10.1021/ja307083b

Activity-based protein profiling: The serine hydrolases
journal, December 1999

  • Liu, Y.; Patricelli, M. P.; Cravatt, B. F.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 26
  • DOI: 10.1073/pnas.96.26.14694

Activity-Based Profiling of Proteases
journal, June 2014


Activity-Based Probes for the Study of Proteases: Recent Advances and Developments
journal, March 2012


Activity-based probes for the proteomic profiling of metalloproteases
journal, June 2004

  • Saghatelian, A.; Jessani, N.; Joseph, A.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 27
  • DOI: 10.1073/pnas.0402784101

Functional Interrogation of the Kinome Using Nucleotide Acyl Phosphates
journal, January 2007

  • Patricelli, Matthew P.; Szardenings, A. Katrin; Liyanage, Marek
  • Biochemistry, Vol. 46, Issue 2
  • DOI: 10.1021/bi062142x

Activity-Based Protein Profiling Reveals Mitochondrial Oxidative Enzyme Impairment and Restoration in Diet-Induced Obese Mice
journal, October 2012


Chemical Proteomic Probes for Profiling Cytochrome P450 Activities and Drug Interactions In Vivo
journal, September 2007


Activity-based probes for proteomic profiling of histone deacetylase complexes
journal, January 2007

  • Salisbury, C. M.; Cravatt, B. F.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 4
  • DOI: 10.1073/pnas.0608659104

Optimization of Activity-Based Probes for Proteomic Profiling of Histone Deacetylase Complexes
journal, February 2008

  • Salisbury, Cleo M.; Cravatt, Benjamin F.
  • Journal of the American Chemical Society, Vol. 130, Issue 7
  • DOI: 10.1021/ja074138u

An Inhibitor of Glutathione S-Transferase Omega 1 that Selectively Targets Apoptotic Cells
journal, July 2012

  • Pace, Nicholas J.; Pimental, Daniel R.; Weerapana, Eranthie
  • Angewandte Chemie International Edition, Vol. 51, Issue 33
  • DOI: 10.1002/anie.201203730

Active-site Peptide “Fingerprinting” of Glycosidases in Complex Mixtures by Mass Spectrometry
journal, August 2005

  • Hekmat, Omid; Kim, Young-Wan; Williams, Spencer J.
  • Journal of Biological Chemistry, Vol. 280, Issue 42
  • DOI: 10.1074/jbc.M508434200

A Mechanism-Based ICAT Strategy for Comparing Relative Expression and Activity Levels of Glycosidases in Biological Systems
journal, August 2008

  • Hekmat, Omid; He, Shouming; Warren, R. Antony J.
  • Journal of Proteome Research, Vol. 7, Issue 8
  • DOI: 10.1021/pr7008302

Suite of Activity-Based Probes for Cellulose-Degrading Enzymes
journal, December 2012

  • Chauvigné-Hines, Lacie M.; Anderson, Lindsey N.; Weaver, Holly M.
  • Journal of the American Chemical Society, Vol. 134, Issue 50
  • DOI: 10.1021/ja309790w

Activity-Based Profiling of Retaining β-Glucosidases: A Comparative Study
journal, April 2011

  • Witte, Martin D.; Walvoort, Marthe T. C.; Li, Kah-Yee
  • ChemBioChem, Vol. 12, Issue 8
  • DOI: 10.1002/cbic.201000773

Building better bioorthogonal reactions
journal, August 2014

  • Shih, Hui-Wen; Kamber, David N.; Prescher, Jennifer A.
  • Current Opinion in Chemical Biology, Vol. 21
  • DOI: 10.1016/j.cbpa.2014.07.002

Applications of Copper-Catalyzed Click Chemistry in Activity-Based Protein Profiling
journal, January 2014


The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

  • Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1178

Genomics of wood-degrading fungi
journal, November 2014


Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30
journal, January 2013

  • Anderson, Lindsey N.; Culley, David E.; Hofstad, Beth A.
  • Molecular BioSystems, Vol. 9, Issue 12
  • DOI: 10.1039/c3mb70333a

Investigation of the active site of Escherichia coli β-d-galactosidase by photoaffinity labelling
journal, August 1992


A Strategy for Functional Proteomic Analysis of Glycosidase Activity from Cell Lysates
journal, October 2004

  • Vocadlo, David J.; Bertozzi, Carolyn R.
  • Angewandte Chemie International Edition, Vol. 43, Issue 40
  • DOI: 10.1002/anie.200454235

Synthesis and Testing of Mechanism-Based Protein-Profiling Probes for Retaining Endo-glycosidases
journal, January 2006

  • Williams, Spencer J.; Hekmat, Omid; Withers, Stephen G.
  • ChemBioChem, Vol. 7, Issue 1
  • DOI: 10.1002/cbic.200500279

Fluorescently labeled inhibitor for profiling cytoplasmic peptide:N-glycanase
journal, July 2007

  • Hagihara, Shinya; Miyazaki, Ayako; Matsuo, Ichiro
  • Glycobiology, Vol. 17, Issue 10
  • DOI: 10.1093/glycob/cwm079

Synthesis and Use of Mechanism-Based Protein-Profiling Probes for Retaining β- d -Glucosaminidases Facilitate Identification of Pseudomonas aeruginosa NagZ
journal, January 2008

  • Stubbs, Keith A.; Scaffidi, Adrian; Debowski, Aleksandra W.
  • Journal of the American Chemical Society, Vol. 130, Issue 1
  • DOI: 10.1021/ja0763605

A general method for affinity-based proteomic profiling of exo-α-glycosidases
journal, January 2011

  • Gandy, Michael N.; Debowski, Aleksandra W.; Stubbs, Keith A.
  • Chemical Communications, Vol. 47, Issue 17
  • DOI: 10.1039/c1cc10308c

A mechanism-based inactivator of glycoside hydrolases involving formation of a transient non-classical carbocation
journal, December 2014

  • Chakladar, Saswati; Wang, Yi; Clark, Thomas
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms6590

Novozym 435-catalyzed synthesis of fatty acid ethyl esters from soybean oil for biodiesel production
journal, February 2014


Biodiesel synthesis combining pre-esterification with alkali catalyzed process from rapeseed oil deodorizer distillate
journal, July 2009


Microbial biodiesel production by direct methanolysis of oleaginous biomass
journal, April 2014


Study of the microwave lipid extraction from microalgae for biodiesel production
journal, August 2014


Biodiesel as feasible petrol fuel replacement: a multidisciplinary overview
journal, January 2010

  • Luque, Rafael; Lovett, Jon C.; Datta, Bipasa
  • Energy & Environmental Science, Vol. 3, Issue 11
  • DOI: 10.1039/c0ee00085j

Lipase-catalyzed process for biodiesel production: Protein engineering and lipase production: Lipase-Catalyzed Process for Biodiesel Production
journal, December 2013

  • Hwang, Hyun Tae; Qi, Feng; Yuan, Chongli
  • Biotechnology and Bioengineering, Vol. 111, Issue 4
  • DOI: 10.1002/bit.25162

Techniques to measure lipase and esterase activity in vitro
journal, June 2005


An activity-based probe for high-throughput measurements of triacylglycerol lipases
journal, July 2011


Design and synthesis of triglyceride analogue biotinylated suicide inhibitors for directed molecular evolution of lipolytic enzymes
journal, September 2000


A versatile library of activity-based probes for fluorescence detection and/or affinity isolation of lipolytic enzymes
journal, October 2006


Lipolytic and esterolytic activity-based profiling of murine liver
journal, September 2008

  • Birner-Gruenberger, Ruth; Susani-Etzerodt, Heidrun; Kollroser, Manfred
  • PROTEOMICS, Vol. 8, Issue 17
  • DOI: 10.1002/pmic.200800191

Activity-Based Proteomics of Lipolytic Enzymes
journal, June 2007


Activity based subcellular resolution imaging of lipases
journal, January 2012

  • Viertler, Martin; Schittmayer, Matthias; Birner-Gruenberger, Ruth
  • Bioorganic & Medicinal Chemistry, Vol. 20, Issue 2
  • DOI: 10.1016/j.bmc.2011.04.018

Latest trends in feedstocks for biodiesel production
journal, August 2013

  • Pinzi, Sara; Leiva, David; López-García, Isabel
  • Biofuels, Bioproducts and Biorefining, Vol. 8, Issue 1
  • DOI: 10.1002/bbb.1435

Manipulating Fatty Acid Biosynthesis in Microalgae for Biofuel through Protein-Protein Interactions
journal, September 2012


Proteome-Wide Reactivity Profiling Identifies Diverse Carbamate Chemotypes Tuned for Serine Hydrolase Inhibition
journal, May 2013

  • Chang, Jae Won; Cognetta, Armand B.; Niphakis, Micah J.
  • ACS Chemical Biology, Vol. 8, Issue 7
  • DOI: 10.1021/cb400261h

Thioredoxin-linked processes in cyanobacteria are as numerous as in chloroplasts, but targets are different
journal, December 2003

  • Lindahl, M.; Florencio, F. J.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 26, p. 16107-16112
  • DOI: 10.1073/pnas.2534397100

Protein Thiol Modifications Visualized In Vivo
journal, October 2004


Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium
journal, October 2013

  • Sadler, Natalie C.; Melnicki, Matthew R.; Serres, Margrethe H.
  • ACS Chemical Biology, Vol. 9, Issue 1
  • DOI: 10.1021/cb400769v

Thiol-based redox proteins in abscisic acid and methyl jasmonate signaling in Brassica napus guard cells
journal, April 2014

  • Zhu, Mengmeng; Zhu, Ning; Song, Wen-yuan
  • The Plant Journal, Vol. 78, Issue 3
  • DOI: 10.1111/tpj.12490

Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria
journal, July 2014


Fifty years in the thioredoxin field and a bountiful harvest
journal, November 2012

  • Buchanan, Bob B.; Holmgren, Arne; Jacquot, Jean-Pierre
  • Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1820, Issue 11
  • DOI: 10.1016/j.bbagen.2012.07.006

Sustained H2 Production Driven by Photosynthetic Water Splitting in a Unicellular Cyanobacterium
journal, August 2012

  • Melnicki, Matthew R.; Pinchuk, Grigoriy E.; Hill, Eric A.
  • mBio, Vol. 3, Issue 4
  • DOI: 10.1128/mBio.00197-12

Protein Phosphorylation on Ser, Thr and Tyr Residues in Cyanobacteria
journal, January 2005

  • Zhang, Cheng-Cai; Jang, Jichan; Sakr, Samer
  • Journal of Molecular Microbiology and Biotechnology, Vol. 9, Issue 3-4
  • DOI: 10.1159/000089644

Nanomolar affinity, iminosugar-based chemical probes for specific labeling of lysosomal glucocerebrosidase
journal, January 2010

  • Scherpenzeel, Monique van; van den Berg, Richard J. B. H. N.; Donker-Koopman, Wilma E.
  • Bioorganic & Medicinal Chemistry, Vol. 18, Issue 1
  • DOI: 10.1016/j.bmc.2009.10.060

Ultrasensitive in situ visualization of active glucocerebrosidase molecules
journal, October 2010

  • Witte, Martin D.; Kallemeijn, Wouter W.; Aten, Jan
  • Nature Chemical Biology, Vol. 6, Issue 12
  • DOI: 10.1038/nchembio.466

Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum
journal, August 2012

  • Wiedner, Susan D.; Burnum, Kristin E.; Pederson, LeeAnna M.
  • Journal of Biological Chemistry, Vol. 287, Issue 40
  • DOI: 10.1074/jbc.M112.394106

Profiling Serine Hydrolase Activities in Complex Proteomes
journal, April 2001

  • Kidd, Dana; Liu, Yongsheng; Cravatt, Benjamin F.
  • Biochemistry, Vol. 40, Issue 13
  • DOI: 10.1021/bi002579j

Orlistat Is a Novel Inhibitor of Fatty Acid Synthase with Antitumor Activity
journal, March 2004


Inhibitor and Protein Microarrays for Activity-Based Recognition of Lipolytic Enzymes
journal, February 2006

  • Schmidinger, Hannes; Susani-Etzerodt, Heidrun; Birner-Gruenberger, Ruth
  • ChemBioChem, Vol. 7, Issue 3
  • DOI: 10.1002/cbic.200500276

Modulation of Fatty Acid Synthase Enzyme Activity and Expression during Hepatitis C Virus Replication
journal, April 2013