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Title: Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions

Abstract

Polysaccharide degradation by marine microbes represents one of the largest and most rapid heterotrophic transformations of organic matter in the environment. Microbes employ systems of complementary carbohydrate-specific enzymes to deconstruct algal or plant polysaccharides (glycans) into monosaccharides. Because of the high diversity of glycan substrates, the functions of these enzymes are often difficult to establish. One solution to this problem may lie within naturally occurring microdiversity; varying numbers of enzymes, due to gene loss, duplication, or transfer, among closely related environmental microbes create metabolic differences akin to those generated by knock-out strains engineered in the laboratory used to establish the functions of unknown genes. Inspired by this natural fine-scale microbial diversity, we show here that it can be used to develop hypotheses guiding biochemical experiments for establishing the role of these enzymes in nature. In this work, we investigated alginate degradation among closely related strains of the marine bacterium Vibrio splendidus. One strain, V. splendidus 13B01, exhibited high extracellular alginate lyase activity compared with other V. splendidus strains. To identify the enzymes responsible for this high extracellular activity, we compared V. splendidus 13B01 with the previously characterized V. splendidus 12B01, which has low extracellular activity and lacks two alginate lyasemore » genes present in V. splendidus 13B01. Using a combination of genomics, proteomics, biochemical, and functional screening, we identified a polysaccharide lyase family 7 enzyme that is unique to V. splendidus 13B01, secreted, and responsible for the rapid digestion of extracellular alginate. These results demonstrate the value of querying the enzymatic repertoires of closely related microbes to rapidly pinpoint key proteins with beneficial functions.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [3];  [4];  [1]
  1. Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Chemical and Biomolecular Engineering
  2. Ernst Moritz Arndt Univ. of Greifswald, Greifswald (Germany). Pharmaceutical Biotechnology, Inst. of Pharmacy
  3. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering
  4. Univ. of Bremen (MARUM), Bremen (Germany). Center for Marine Environmental Sciences
Publication Date:
Research Org.:
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1535360
Grant/Contract Number:  
SC0008743
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 292; Journal Issue: 31; 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; Biochemistry & Molecular Biology

Citation Formats

Badur, Ahmet H., Plutz, Matthew J., Yalamanchili, Geethika, Jagtap, Sujit Sadashiv, Schweder, Thomas, Unfried, Frank, Markert, Stephanie, Polz, Martin F., Hehemann, Jan-Hendrik, and Rao, Christopher V. Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions. United States: N. p., 2017. Web. doi:10.1074/jbc.m117.787192.
Badur, Ahmet H., Plutz, Matthew J., Yalamanchili, Geethika, Jagtap, Sujit Sadashiv, Schweder, Thomas, Unfried, Frank, Markert, Stephanie, Polz, Martin F., Hehemann, Jan-Hendrik, & Rao, Christopher V. Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions. United States. doi:10.1074/jbc.m117.787192.
Badur, Ahmet H., Plutz, Matthew J., Yalamanchili, Geethika, Jagtap, Sujit Sadashiv, Schweder, Thomas, Unfried, Frank, Markert, Stephanie, Polz, Martin F., Hehemann, Jan-Hendrik, and Rao, Christopher V. Wed . "Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions". United States. doi:10.1074/jbc.m117.787192. https://www.osti.gov/servlets/purl/1535360.
@article{osti_1535360,
title = {Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions},
author = {Badur, Ahmet H. and Plutz, Matthew J. and Yalamanchili, Geethika and Jagtap, Sujit Sadashiv and Schweder, Thomas and Unfried, Frank and Markert, Stephanie and Polz, Martin F. and Hehemann, Jan-Hendrik and Rao, Christopher V.},
abstractNote = {Polysaccharide degradation by marine microbes represents one of the largest and most rapid heterotrophic transformations of organic matter in the environment. Microbes employ systems of complementary carbohydrate-specific enzymes to deconstruct algal or plant polysaccharides (glycans) into monosaccharides. Because of the high diversity of glycan substrates, the functions of these enzymes are often difficult to establish. One solution to this problem may lie within naturally occurring microdiversity; varying numbers of enzymes, due to gene loss, duplication, or transfer, among closely related environmental microbes create metabolic differences akin to those generated by knock-out strains engineered in the laboratory used to establish the functions of unknown genes. Inspired by this natural fine-scale microbial diversity, we show here that it can be used to develop hypotheses guiding biochemical experiments for establishing the role of these enzymes in nature. In this work, we investigated alginate degradation among closely related strains of the marine bacterium Vibrio splendidus. One strain, V. splendidus 13B01, exhibited high extracellular alginate lyase activity compared with other V. splendidus strains. To identify the enzymes responsible for this high extracellular activity, we compared V. splendidus 13B01 with the previously characterized V. splendidus 12B01, which has low extracellular activity and lacks two alginate lyase genes present in V. splendidus 13B01. Using a combination of genomics, proteomics, biochemical, and functional screening, we identified a polysaccharide lyase family 7 enzyme that is unique to V. splendidus 13B01, secreted, and responsible for the rapid digestion of extracellular alginate. These results demonstrate the value of querying the enzymatic repertoires of closely related microbes to rapidly pinpoint key proteins with beneficial functions.},
doi = {10.1074/jbc.m117.787192},
journal = {Journal of Biological Chemistry},
number = 31,
volume = 292,
place = {United States},
year = {2017},
month = {6}
}

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