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Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS)

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    Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS)
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    † Joint BioEnergy Institute, Emeryville, California 94608, United States
    ‡ Sandia National Laboratories, Livermore, California 94551, United States
    § Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
    ∥ Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
    ⊥ Joint Genome Institute, Walnut Creek, California 94598, United States
    # University of California, Berkeley, California 94720, United States
    *(K.D.) E-mail: [email protected]
    *(B.G.F.) E-mail: [email protected]
    *(T.R.N.) E-mail: [email protected]
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    ACS Chemical Biology

    Cite this: ACS Chem. Biol. 2014, 9, 7, 1470–1479
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    https://doi.org/10.1021/cb5000289
    Published May 12, 2014
    Copyright © 2014 American Chemical Society
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    Abstract

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    Glycoside hydrolases (GHs) are critical to cycling of plant biomass in the environment, digestion of complex polysaccharides by the human gut microbiome, and industrial activities such as deployment of cellulosic biofuels. High-throughput sequencing methods show tremendous sequence diversity among GHs, yet relatively few examples from the over 150,000 unique domain arrangements containing GHs have been functionally characterized. Here, we show how cell-free expression, bioconjugate chemistry, and surface-based mass spectrometry can be used to study glycoside hydrolase reactions with plant biomass. Detection of soluble products is achieved by coupling a unique chemical probe to the reducing end of oligosaccharides in a stable oxime linkage, while the use of 13C-labeled monosaccharide standards (xylose and glucose) allows quantitation of the derivatized glycans. We apply this oxime-based nanostructure-initiator mass spectrometry (NIMS) method to characterize the functional diversity of GHs secreted by Clostridium thermocellum, a model cellulolytic organism. New reaction specificities are identified, and differences in rates and yields of individual enzymes are demonstrated in reactions with biomass substrates. Numerical analyses of time series data suggests that synergistic combinations of mono- and multifunctional GHs can decrease the complexity of enzymes needed for the hydrolysis of plant biomass during the production of biofuels.

    Copyright © 2014 American Chemical Society

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    Description of substrate synthesis, figures, and tables. This material is available free of charge via the Internet at http://pubs.acs.org.

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    Cite this: ACS Chem. Biol. 2014, 9, 7, 1470–1479
    Click to copy citationCitation copied!
    https://doi.org/10.1021/cb5000289
    Published May 12, 2014
    Copyright © 2014 American Chemical Society
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