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

BMC Genomics

Research Article

Gerald A Tuskan¹  Xiaohan Yang¹  John P Vogel²  Jennifer N Bragg²  Jiajie Wu³  Ludmila Tyler⁴ 

[1] Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA;USDA-ARS Western Regional Research Center, 94710, Albany, CA, USA;USDA-ARS Western Regional Research Center, 94710, Albany, CA, USA;Department of Plant Sciences, University of California, 95616, Davis, CA, USA;USDA-ARS Western Regional Research Center, 94710, Albany, CA, USA;Department of Plant and Microbial Biology, University of California, 94720, Berkeley, CA, USA;

关键词: Pectin;    Chitinases;    Glycoside Hydrolase;    Chitinolytic Activity;    CAZy Database;   

DOI  :  10.1186/1471-2164-11-600

 received in 2010-07-14, accepted in 2010-10-25,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundGlycoside 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 Populustrichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodiumdistachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families.ResultsWe 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. For several glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51), we present a detailed literature review together with an examination of the family structures. This analysis of individual families revealed both similarities and distinctions between monocots and eudicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within GH families, the Brachypodium and sorghum proteins generally cluster with those from other monocots.ConclusionsThis 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 grass 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.

【 授权许可】

Unknown   
© Tyler et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.