Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon.
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, at the levels of the whole genome and 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. 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.


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 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.
Tyler
Ludmila
L
USDA-ARS Western Regional Research Center, Albany, CA 94710, USA.
Bragg
Jennifer N
JN
Wu
Jiajie
J
Yang
Xiaohan
X
Tuskan
Gerald A
GA
Vogel
John P
JP
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D058431:Brachypodium / Q000201:enzymology* / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D006026:Glycoside Hydrolases / Q000737:chemistry / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D012275:Oryza / Q000201:enzymology / Q000235:genetics; D010802:Phylogeny; D032107:Populus / Q000201:enzymology / Q000235:genetics; D016415:Sequence Alignment; D045868:Sorghum / Q000201:enzymology / Q000235:genetics
D006026:Glycoside Hydrolases