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Title: Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon

Abstract

Background Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, both at the whole-genome level and at the level of individual glycoside hydrolase families. Results We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. Examination of individual glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51) revealed both similarities and distinctions betweenmore » monocots and dicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. Conclusions This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a monocot model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.« less

Authors:
 [1];  [1];  [1];  [2];  [2];  [1]
  1. United States Department of Agriculture (USDA), Western Regional Research Center (WRRC), Albany
  2. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1023290
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1471--2164
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ANIMALS; ARABIDOPSIS; CARBOHYDRATES; CELL WALL; CEREALS; COMPARATIVE EVALUATIONS; CROPS; ENZYMES; FUNCTIONALS; GENES; GLYCOSIDES; HYDROLASES; LIPIDS; METABOLISM; PROTEINS; RICE; SORGHUM; STARCH; TREES

Citation Formats

Tyler, Ludmila, Bragg, Jennifer, Wu, Jiajie, Yang, Xiaohan, Tuskan, Gerald A, and Vogel, John. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. United States: N. p., 2010. Web. doi:10.1186/1471-2164-11-600.
Tyler, Ludmila, Bragg, Jennifer, Wu, Jiajie, Yang, Xiaohan, Tuskan, Gerald A, & Vogel, John. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. United States. doi:10.1186/1471-2164-11-600.
Tyler, Ludmila, Bragg, Jennifer, Wu, Jiajie, Yang, Xiaohan, Tuskan, Gerald A, and Vogel, John. Fri . "Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon". United States. doi:10.1186/1471-2164-11-600.
@article{osti_1023290,
title = {Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon},
author = {Tyler, Ludmila and Bragg, Jennifer and Wu, Jiajie and Yang, Xiaohan and Tuskan, Gerald A and Vogel, John},
abstractNote = {Background Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, both at the whole-genome level and at the level of individual glycoside hydrolase families. Results We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. Examination of individual glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51) revealed both similarities and distinctions between monocots and dicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. Conclusions This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a monocot model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.},
doi = {10.1186/1471-2164-11-600},
journal = {BMC Genomics},
issn = {1471--2164},
number = 1,
volume = 11,
place = {United States},
year = {2010},
month = {1}
}