Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases

Glasgow, Evan M.; Vander Meulen, Kirk A.; Takasuka, Taichi E.; Bianchetti, Christopher M.; Bergeman, Lai F.; Deutsch, Samuel; Fox, Brian G.

doi:10.1016/j.jmb.2019.01.024

Title: Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases

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Abstract

Some glycoside hydrolases have broad specificity for hydrolysis of glycosidic bonds, potentially increasing their functional utility and flexibility in physiological and industrial applications. Here, to deepen the understanding of the structural and evolutionary driving forces underlying specificity patterns in glycoside hydrolase family 5, we quantitatively screened the activity of the catalytic core domains from subfamily 4 (GH5_4) and closely related enzymes on four substrates: lichenan, xylan, mannan, and xyloglucan. Phylogenetic analysis revealed that GH5_4 consists of three major clades, and one of these clades, referred to here as clade 3, displayed average specific activities of 4.2 and 1.2 U/mg on lichenan and xylan, approximately 1 order of magnitude larger than the average for active enzymes in clades 1 and 2. Enzymes in clade 3 also more consistently met assay detection thresholds for reaction with all four substrates. We also identified a subfamily-wide positive correlation between lichenase and xylanase activities, as well as a weaker relationship between lichenase and xyloglucanase. To connect these results to structural features, we used the structure of CelE from Hungateiclostridium thermocellum (PDB 4IM4) as an example clade 3 enzyme with activities on all four substrates. Comparison of the sequence and structure of this enzyme with othersmore »« less

Authors:

Glasgow, Evan M. ^[1]; Vander Meulen, Kirk A. ^[1]; Takasuka, Taichi E. ^[2]; Bianchetti, Christopher M. ^[3]; Bergeman, Lai F. ^[1]; Deutsch, Samuel ^[4]; Fox, Brian G. ^[1]

Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry
Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry; Hokkaido Univ., Sapporo (Japan). Research Faculty of Agriculture
Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry; Univ. of Wisconsin, Oshkosh, WI (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:: Fri Mar 15 00:00:00 EDT 2019

Research Org.:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Contributing Org.:: UW-Madison Center for High Throughput Computing (CHTC) in the Department of Computer Sciences

OSTI Identifier:: 1546759

Alternate Identifier(s):: OSTI ID: 1635982

Grant/Contract Number:: SC0018409; FC02-07ER64494; AC02-05CH11231; 5 T32 GM008349

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Molecular Biology

Additional Journal Information:: Journal Volume: 431; Journal Issue: 6; Journal ID: ISSN 0022-2836

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; glycoside hydrolase; substrate specificity; polysaccharide; protein evolution; synthetic biology

Citation Formats


                    Glasgow, Evan M., Vander Meulen, Kirk A., Takasuka, Taichi E., Bianchetti, Christopher M., Bergeman, Lai F., Deutsch, Samuel, and Fox, Brian G. Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases.  United States: N. p., 2019. 
Web.  doi:10.1016/j.jmb.2019.01.024.

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                    Glasgow, Evan M., Vander Meulen, Kirk A., Takasuka, Taichi E., Bianchetti, Christopher M., Bergeman, Lai F., Deutsch, Samuel, & Fox, Brian G. Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases.  United States.  https://doi.org/10.1016/j.jmb.2019.01.024

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                    Glasgow, Evan M., Vander Meulen, Kirk A., Takasuka, Taichi E., Bianchetti, Christopher M., Bergeman, Lai F., Deutsch, Samuel, and Fox, Brian G. Fri .  
"Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases".  United States.  https://doi.org/10.1016/j.jmb.2019.01.024.  https://www.osti.gov/servlets/purl/1546759.

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@article{osti_1546759,

  title        = {Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases},

  author       = {Glasgow, Evan M. and Vander Meulen, Kirk A. and Takasuka, Taichi E. and Bianchetti, Christopher M. and Bergeman, Lai F. and Deutsch, Samuel and Fox, Brian G.},

  abstractNote = {Some glycoside hydrolases have broad specificity for hydrolysis of glycosidic bonds, potentially increasing their functional utility and flexibility in physiological and industrial applications. Here, to deepen the understanding of the structural and evolutionary driving forces underlying specificity patterns in glycoside hydrolase family 5, we quantitatively screened the activity of the catalytic core domains from subfamily 4 (GH5_4) and closely related enzymes on four substrates: lichenan, xylan, mannan, and xyloglucan. Phylogenetic analysis revealed that GH5_4 consists of three major clades, and one of these clades, referred to here as clade 3, displayed average specific activities of 4.2 and 1.2 U/mg on lichenan and xylan, approximately 1 order of magnitude larger than the average for active enzymes in clades 1 and 2. Enzymes in clade 3 also more consistently met assay detection thresholds for reaction with all four substrates. We also identified a subfamily-wide positive correlation between lichenase and xylanase activities, as well as a weaker relationship between lichenase and xyloglucanase. To connect these results to structural features, we used the structure of CelE from Hungateiclostridium thermocellum (PDB 4IM4) as an example clade 3 enzyme with activities on all four substrates. Comparison of the sequence and structure of this enzyme with others throughout GH5_4 and neighboring subfamilies reveals at least two residues (H149 and W203) that are linked to strong activity across the substrates. Placing GH5_4 in context with other related subfamilies, we highlight several possibilities for the ongoing evolutionary specialization of GH5_4 enzymes.},

  doi          = {10.1016/j.jmb.2019.01.024},

  journal      = {Journal of Molecular Biology},

  number       = 6,

  volume       = 431,

  place        = {United States},

  year         = {Fri Mar 15 00:00:00 EDT 2019},

  month        = {Fri Mar 15 00:00:00 EDT 2019}

}

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