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

Tyler L, Bragg JN, Wu J, Yang X, Tuskan GA, Vogel JP - BMC Genomics (2010)

Bottom Line: Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes.We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families.This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA-ARS Western Regional Research Center, Albany, CA 94710, USA.

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, 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.

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The GH28 family of polygalacturonases. The tree includes GH28 proteins from Arabidopsis (AT), rice, Brachypodium (Bradi), sorghum, poplar, and maize. Tree construction and color-coding (blue for eudicots and red for grasses) are as in Figure 2. For several branches, the percent of bootstrap replicates supporting the branch is indicated. Dotted and solid gray lines mark groups according to the designations of Penning et al. [90]. Small gray arrows indicate proteins corresponding to genes - QRT2, ADPG1 and ADPG2 in group D and At1g48100 in group C - characterized by Ogawa et al. [84]. A gray asterisk marks a clade of grass sequences that does not fall into any of the other groups. For clarity, names are shown only for selected Arabidopsis and Brachypodium genes. For complete branch labels and bootstrap values, see additional file 14.
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Figure 6: The GH28 family of polygalacturonases. The tree includes GH28 proteins from Arabidopsis (AT), rice, Brachypodium (Bradi), sorghum, poplar, and maize. Tree construction and color-coding (blue for eudicots and red for grasses) are as in Figure 2. For several branches, the percent of bootstrap replicates supporting the branch is indicated. Dotted and solid gray lines mark groups according to the designations of Penning et al. [90]. Small gray arrows indicate proteins corresponding to genes - QRT2, ADPG1 and ADPG2 in group D and At1g48100 in group C - characterized by Ogawa et al. [84]. A gray asterisk marks a clade of grass sequences that does not fall into any of the other groups. For clarity, names are shown only for selected Arabidopsis and Brachypodium genes. For complete branch labels and bootstrap values, see additional file 14.

Mentions: To investigate the evolutionary history of the GH28 family, we constructed a phylogenetic tree based on protein sequences from Arabidopsis, rice, Brachypodium, sorghum, poplar, and maize (Figure 6 and additional file 14). The maize sequences were as identified by Penning et al. [90], except that the proteins encoded by AC210013.4 and AC231180.2 were omitted from the analysis, because they did not contain Pfam-predicted GH domains. For ease of reference, groups of GH28 proteins are labeled with the designations used by Penning et al. for Arabidopsis, rice, and maize [90]. These labels are included here to simplify comparisons across studies and do not necessarily correlate precisely with the clades of the six-species tree shown in Figure 6. For instance, while Group A has 100% bootstrap support, Group E as identified by Penning et al. [90] is split into two clades in our phylogenetic tree and is more appropriately regarded as part of the larger E/F/H clade (Figure 6 and additional file 14). The proteins encoded by QRT2, ADPG1 and ADPG2 fall into group D and the At1g48100-encoded protein into group C (Figure 6).


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

Tyler L, Bragg JN, Wu J, Yang X, Tuskan GA, Vogel JP - BMC Genomics (2010)

The GH28 family of polygalacturonases. The tree includes GH28 proteins from Arabidopsis (AT), rice, Brachypodium (Bradi), sorghum, poplar, and maize. Tree construction and color-coding (blue for eudicots and red for grasses) are as in Figure 2. For several branches, the percent of bootstrap replicates supporting the branch is indicated. Dotted and solid gray lines mark groups according to the designations of Penning et al. [90]. Small gray arrows indicate proteins corresponding to genes - QRT2, ADPG1 and ADPG2 in group D and At1g48100 in group C - characterized by Ogawa et al. [84]. A gray asterisk marks a clade of grass sequences that does not fall into any of the other groups. For clarity, names are shown only for selected Arabidopsis and Brachypodium genes. For complete branch labels and bootstrap values, see additional file 14.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091745&req=5

Figure 6: The GH28 family of polygalacturonases. The tree includes GH28 proteins from Arabidopsis (AT), rice, Brachypodium (Bradi), sorghum, poplar, and maize. Tree construction and color-coding (blue for eudicots and red for grasses) are as in Figure 2. For several branches, the percent of bootstrap replicates supporting the branch is indicated. Dotted and solid gray lines mark groups according to the designations of Penning et al. [90]. Small gray arrows indicate proteins corresponding to genes - QRT2, ADPG1 and ADPG2 in group D and At1g48100 in group C - characterized by Ogawa et al. [84]. A gray asterisk marks a clade of grass sequences that does not fall into any of the other groups. For clarity, names are shown only for selected Arabidopsis and Brachypodium genes. For complete branch labels and bootstrap values, see additional file 14.
Mentions: To investigate the evolutionary history of the GH28 family, we constructed a phylogenetic tree based on protein sequences from Arabidopsis, rice, Brachypodium, sorghum, poplar, and maize (Figure 6 and additional file 14). The maize sequences were as identified by Penning et al. [90], except that the proteins encoded by AC210013.4 and AC231180.2 were omitted from the analysis, because they did not contain Pfam-predicted GH domains. For ease of reference, groups of GH28 proteins are labeled with the designations used by Penning et al. for Arabidopsis, rice, and maize [90]. These labels are included here to simplify comparisons across studies and do not necessarily correlate precisely with the clades of the six-species tree shown in Figure 6. For instance, while Group A has 100% bootstrap support, Group E as identified by Penning et al. [90] is split into two clades in our phylogenetic tree and is more appropriately regarded as part of the larger E/F/H clade (Figure 6 and additional file 14). The proteins encoded by QRT2, ADPG1 and ADPG2 fall into group D and the At1g48100-encoded protein into group C (Figure 6).

Bottom Line: Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes.We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families.This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA-ARS Western Regional Research Center, Albany, CA 94710, USA.

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, 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.

Show MeSH
Related in: MedlinePlus